ex) $>>ave_vol test.sdt test_out.sdt 100<RET>
-----------------------------------------------------------------------
avstim
---------- Vstim program Ver.0.0 --------
usage: vstim sequence_filename <RET>
usage: vstim -t <RET>
-t : Test mode with a small window
----------------------------------------------------------
Compiled [Oct 29 13:57:35 2015] Edited [Oct 29 13:55:24 2015]
bd
bd [age check script ver. 0.1 20.Jan.2014]
--------------------------------------------
bd [birthday]<RET>
bd [birthday] [date for the age calculation]<RET>
>bd 19701231<RET>
>bd 19701231 20000101<RET>
>bd s451231<RET>
s:showa or h:heisei can be used for the birthday string.
beep
bfdump
#######################################################################
# Dump bflog [ver.0.00] 4.Aug.2011 #
#######################################################################
Usage: bfdump bflog_file_name<RET>
bflip _PDF_
---------- bit flipping program Ver.0.00[12.Jul.2014] --------
usage: bflip input_file_name output_file_name
input-file : any binary
output-file : bit-flipped data
-----------------------------------------------------------------------
binchar
---------- Make 1 byte int binary file program Ver.0.12 ---------------
usage: binchar output_file_name d1 d2 d3 ...
output-file : 1 byte int binary data
-----------------------------------------------------------------------
Compiled [Jul 3 15:26:57 2014] Edited [Jul 3 15:26:11 2014]
binfloat
---------- Make float binary file program Ver.0.13 --------------------
usage: binfloat output_file_name d1 d2 d3 ...
output-file : 4 byte float data
--name for the special numbers --
nan,NAN : not a number (quiet nan, 0x7fc00000)
snan,SNAN : not a number (signaling nan, 0x7f800001)
inf,INF : positive infinity
-inf,-INF : negative infinity
-----------------------------------------------------------------------
Compiled [Jul 3 15:26:57 2014] Edited [Jul 3 15:26:11 2014]
binint
---------- Make int binary file program Ver.0.12 ----------------------
usage: binint output_file_name d1 d2 d3 ...
output-file : 4 byte SIGNED INT binary data
-----------------------------------------------------------------------
Compiled [Jul 3 15:26:58 2014] Edited [Jul 3 15:26:11 2014]
binsint
---------- Make short binary file program Ver.0.12 --------------------
usage: binsint output_file_name d1 d2 d3 ...
output-file : 2 byte SIGNED SHORT binary data
-----------------------------------------------------------------------
Compiled [Jul 3 15:26:56 2014] Edited [Jul 3 15:26:11 2014]
binuchar
---------- Make 1 byte unsigned int binary file program Ver.0.12 --------
usage: binuchar output_file_name d1 d2 d3 ...
output-file : 1 byte unsigned int binary data
-------------------------------------------------------------------------
Compiled [Jul 3 15:26:58 2014] Edited [Jul 3 15:26:11 2014]
binuint
---------- Make unsigned int binary file program Ver.0.01 ---------------------
usage: binint output_file_name d1 d2 d3 ...
output-file : 4 byte UNSIGNED INT binary data
-------------------------------------------------------------------------------
Compiled [Jul 3 15:26:58 2014] Edited [Jul 3 15:26:11 2014]
binusint
---------- Make unsigned short binary file program Ver.0.01 -----------
usage: binusint output_file_name d1 d2 d3 ...
output-file : 2 byte UNSIGNED SHORT binary data
-----------------------------------------------------------------------
Compiled [Jul 3 15:26:59 2014] Edited [Jul 3 15:26:11 2014]
bit2byte
---------- bit > byte conversion program Ver.0.0 --------
usage: bit2byte input_file_name output_file_name (-)
input-file : bit data
output-file : 1 byte data(0 or 1)
'-' flag : to make reverse order bits(1-8 -> 8->1)
----------------------------------------------------------
Compiled [Feb 19 16:31:38 2016] Edited [Feb 19 16:31:32 2016]
blfilt
blfilt v0.00
********************************************************************
2D bilateral filter application on sdt/spr files
Usage: blfilt Input_filenamebody (fwhm1) (fwhm2)
filter_size is 5x5
fwhm1 : FWHM inplane(default:2)
fwhm2 : FWHM in intensity space(FWHM2 = fwhm2 x 2 x sigma x sqrt(2ln2) ~ fwhm2 x 2.35 x sigma) (default:3)
EX) If you have
blfilt data<RET>
blfilt data 2 3<RET>
********************************************************************
Compiled [Mar 19 12:33:08 2014] Edited [Mar 19 12:32:49 2014]
boxmask
---------- boxmask program Ver.0.00[7.Mar.2013] --------
usage: boxmask output_sdtfile_namebody x y z xStart xEnd yStart yEnd zStart zEnd (-)<RET>
output-file : sdt/spr data
x, y, z : dimension in each axis
xStart xEnd
yStart yEnd
zStart zEnd
- : flag for reversed mask(1>>0, 0>>1)
ex) $>>boxmask vmask 128 128 128 10 100 20 50 0 127<RET>
Output files: vmask.sdt/spr
-----------------------------------------------------------------------
bp_fermi4r
********************************************************************
Usage: bp_fermi Input_file (without .sdt extension) [flag1] [flag2]
flag1 = no. of timecourse periods in your experiment
flag2 = multiple of paradigm frequency for width of Fermi filter (>1000 for only DC)
If flag2 is omitted the default is to just remove the DC component (better known as drift or the Tutus Effect!)
********************************************************************
bp_filt109
bp_filt v1.09 [13/Mar/2009] (w/ fftw3.1.2)
********************************************************************
Usage: bp_filt Input_file (without .sdt extension) [-f -h -l -t]
-f
-h
default=8
-l
-t
Test mode; Filter shape will be shown. No filtering.
EX) If you have
bp_filt data -t -f fermi hanning -h 10 -l 35 30<RET>
bp_filt data -h 10<RET>: highpass only
Cut-off frequency [Hz] = [cut-off value(number of wave)] / [total time for the experiment(sec)]
********************************************************************
bp_filt
bp_filt v1.1.1 [26/Apr/2012] (w/ fftw3.*.*)
********************************************************************
Usage: bp_filt Input_file (without .sdt extension) [-f -h -l -t]
-f
-h
default=8
-l
-dc0
-t
Test mode; Filter shape will be shown. No filtering.
EX) If you have
bp_filt data -t -f fermi hanning -h 10 -l 35 30<RET>
bp_filt data -h 10<RET>: highpass only
Cut-off frequency [Hz] = [cut-off value(number of wave)] / [total time for the experiment(sec)]
********************************************************************
Compiled [Sep 16 17:18:45 2016] Edited [Sep 16 17:18:54 2016]
bsim
---------- bsim (data simulation with beta map) Ver.0.0 ---------------
usage: bsim beta_file model_file (select_flag)
beta_file : beta filename (float; N x nmodel)
model_file : model filename (ascii; num_sample x nmodel)
select_flag : string with 0 or 1 or 2(e.g. 10102, all one for default)
2 is used to put the negative weight(-1) to the model.
output : simulated value file(beta filename + s)
--------------------------------------------------------
Compiled [Apr 14 14:24:26 2015] Edited[Apr 14 14:22:48 2015]
bvfloat
---------- Float data normalization program for BV Ver.0.0 --------
usage: bvfloat input_file_name (output_file_name) (normalize value)
input-file : 4 byte FLOAT data
output-file : 4 byte FLOAT data(Normalized)
normalize value : value for the normalization(default: 7.8)
--------------------------------------------------------------------
Compiled [Mar 19 12:21:16 2014] Edited [Mar 19 12:21:09 2014]
car2model
##############################################
# Model builder ver.0.0 #
##############################################
Usage: car2model car_FILENAME/bit_filename acq_bit_filename (ch_number) (inpulse_response_function) <RET>
ch_number: channel number(1~32)
Example:
$> car2model 160512.car acq.bit 3<RET>
$> car2model 160512.car acq.bit 10 two_gammma.txt <RET>
$> car2model 160512.MRK18.bit acq.bit two_gammma.txt <RET>
Compiled [May 26 14:37:43 2017] Edited [May 26 14:07:51 2017]
car2to1txt
############################################################
# car2to1txt ver.0.1 [Dec. 13 2010] #
############################################################
Usage: car2to1txt FILENAME
Example:
$> car2to1txt 101201.car.txt >101201.car2.txt<RET>
car2txt_new
#########################################################
# Convert .car or .ext data to text form #
#########################################################
Usage: car2txt FILENAME
Output file name is FILENAME + .txt
Example:
$> car2txt 030512.car<RET>
$> car2txt 030512.ext<RET>
v2.0.1
Compiled [Oct 19 16:58:39 2015] Edited [Oct 19 16:58:36 2015]
car2txt
#########################################################
# Convert .car or .ext data to text form #
#########################################################
Usage: car2txt FILENAME
Output file name is FILENAME + .txt
Example:
$> car2txt 030512.car<RET>
$> car2txt 030512.ext<RET>
by Ken(2. Dec. 2010) v2.0.0
caracq
##################################################################
# Acq trigger adjustment tool for .car ver.0.１ [Jan.25 2013] #
##################################################################
Add or Remove acq triggers at the end of acq trigger train.
Usage: caracq FILENAME acquisition_pulse_number
Example:
$> caracq 030512.car 1200<RET>
car_anlz2
##############################################
# Acq trigger analyzer for .car ver.1.4b #
##############################################
Usage: car_anlz FILENAME (-/+)
+: make acq.peak.bit file
-: make acq.peak.bit file as
Example:
$> car_anlz 160512.car<RET>
$> car_anlz 160512.car -<RET>
Compiled [Sep 7 13:57:21 2016] Edited [Sep 7 13:58:30 2016]
car_anlz
##############################################
# Car data analyzer ver.1.4c #
##############################################
Usage: car_anlz FILENAME (+/bit_filename_body)
+: make acq.peak.bit file
-: make acq.peak.bit file as
Example:
$> car_anlz 160512.car <RET>
$> car_anlz 160512.car + <RET>
$> car_anlz 160512.car peak <RET>
Compiled [Nov 9 14:55:14 2016] Edited [Nov 9 14:55:36 2016]
catsdt
----- catsdt ver. 0.0.0 [26.Jan.2013] -----
>>catsdt [filename_body] [filename_body2] <RET>
-----------------------------------------
catvtc
---------------- catvtc Ver.0.00 ----------------
usage: catvtc input_file_name1 input_file_name2 ... input_file_nameN <RET>
input_file_nameN:vtc filename
--------------------------------------------------
Compiled [Jan 16 14:02:05 2014] Edited [Jan 16 14:01:59 2014]
cce
---------- cce (correlation coefficient for binary files) Ver.0.00 --------
usage: cce mapfile_A file_B resultfile (resultfile2)
input-fileA : 4byte float data
input-fileB : ascii data or binary float data
resultfile : 4byte float data(correlation values)
resultfile2 : 4byte float data(p values)
ex) cce run1.sdt prt.txt Result
Number in the protocol file:
@: Neglect the volume
---------------------------------------------------------------------------
Compiled [Jun 13 12:40:48 2016] Edited [Jun 13 12:40:19 2016]
cdd_script
set maindatadir=/usr1/
set datadir=/data/
set curdir=1
if ( == - ) then
if ( -f ~/vnmrsys/global && == - ) then
if ( 0 > = 2 ) then
set year=`date +%Y`
date +%Y
if ( 0 != 1 || 1 == ) then
set userdir=`whoami`
whoami
set fulldir=/usr1/kenji/data/2017
else
cd /usr1/kenji/data/2017
/usr1/kenji/data/2017: No such file or directory.
chdimnii
---------- chdimnii (change dimension for nifti program Ver.0.0) ---------------
usage: chdim nifti_file x y z
data_file : nifti data filename
-------------------------------------------------------
Compiled [Mar 6 10:10:05 2017] Edited[Mar 6 09:52:59 2017]
chdim
---------- chdim (change dimension program Ver.0.0 ---------------
usage: chdim data_file x y z x2 y2 z2 (nv)
data_file : data filename
-------------------------------------------------------
Compiled [Mar 6 10:10:04 2017] Edited[Mar 6 09:52:59 2017]
chk3s
----- chk3s ver. 0.01 [13.Jan.2017] -----
3 orthogonal slice data postprocessing tool
>>chk3s ../raw/gemsir01<RET>
The processed data will appear in the current directory
-----------------------------------------
chkbit
---------- chkbit Ver.0.0.0 -----------------------------------------------------
usage: chkbit bitfile_acq bitfile_car (ntime) (nbin)<RET>
bitfile_acq: acq.bit filename
bitfile_car: cardio/respir.bit filename
ntime: Number of timing in a single TR
nbin: Number of bins
---------------------------------------------------------------------------------
Compiled [Dec 27 15:23:16 2017] Edited [Dec 27 15:28:38 2017]
chnblocks
###############################################################
# Change nblocks for the Fid header [ver.0.0] 21.Oct.2013 #
###############################################################
This program modifies the fid header.
Usage: chnblocks
File Header(32byte):
int nblocks; //# blocks in fid
int ntraces; //# traces per block
int np; //# points per trace
int ebytes; //# bytes per point
int tbytes; //# bytes per trace
int bbytes; //# bytes per block
short transf; //transposed storage flag (not used)
short status; //status of whole file (not used)
int spare1; //reserved for future use (not used)
Block Header(28byte):
short scale; //scaling factor (not used)
short status; //status of data in block (not used)
short index; //block index (not used)
short mode; //mode of data in block (not used)
int ctcount; //ct value for FID (not used)
float lpval; //f2 (2D-f1) left phase in phasefile (not used)
float rpval; //f2 (2D-f1) right phase in phasefile (not used)
float lvl; //level drift correction (not used)
float tlt; //tilt drift correction (not used)
clip
---------- Signed Short data clipping program Ver.0.1[8.Jun.2010] --------
usage: clip input_file_name<RET>
The file will be overwritten.
Negative data is replaced by zero.
-----------------------------------------------------------------------
clusterc
---------- clusterc (cluster size map calculation) Ver.0.0--------
usage: clusterc [input_fname_body] (thre) (cluster_flag) (cluster_size_threshold)<RET>
[input_fname_body].sdt/spr are used as the input.
Output file name: [input_fname_body] -nc.sdt/spr
thre: threshold value (0.5 -- default)
cluster_flag: 1~5(3:default)
1 - 2d4n
2 - 2d8n
3 - 3d6n(default)
4 - 3d18n
5 - 3d26n
6 - 3d116n
cluster_flag>0 for lowercut masking, <0 for uppercut masking
cluster_size_threshold: 0(default:No thresholding) or 1~N
The output file has float type data.
$>clusterc mprage01<RET> is equivalent to $>clusterc mprage01 0.5 3<RET>
-----------------------------------------------------------------
Compiled [Apr 17 12:55:11 2019] Edited [Apr 17 12:55:07 2019]
cmdck
--------------------------------------------
cmdck [command name]
0: Exist
1: Non-exist
--------------------------------------------
conv
conv v1.05
********************************************************************
Usage: conv timing_file (IRFfile) (-) <RET>
If we don't put IRFfile, the shape of timing data will be calculated.
'-' flag can be set for turning off the normalization of the models
---Timing file format---
first-acq-trigger-timing(ms) last-acq-trigger-timing(ms) acq-trigger-number triggers/volume
timing-event1 duration-event1 (weight-event1)
timing-event2 duration-event2 (weight-event2)
timing-event3 duration-event3 (weight-event3)
.........................
.........................
.........................
timing-eventN duration-eventN (weight-eventN)
-------------------------
triggers/volume: shot*slice for 4T data
---Inpulse response function(IRF) file format---
One data for one line. Sampling rate is 100Hz.
-------------------------
********************************************************************
Compiled [Aug 16 09:48:57 2016] Edited [Aug 16 09:50:16 2016]
csadump
#########################################################
# CSA header dump [ver.0.0] 16.Feb.2016 #
#########################################################
This program dumps the siemens csa file.
Usage: csadump
Usage: csadump
Compiled [Feb 16 14:58:25 2016] Edited [Feb 16 14:58:23 2016]
dat2edt
##########################################################
# Convert dat file into edt/epr files [ver.0.1] #
##########################################################
This program converts dat-file to edt/epr files.
Usage: dat2edt
***********************************************************
Compiled [Jul 5 09:23:25 2019] Edited [Jul 5 09:23:20 2019]
dbl2flt
---------- Double>Float conversion program Ver.0.0[24.Sep.2014] --------
usage: dbl2flt input_file_name (output_file_name)
input-file : 8 byte DOUBLE data
output-file : 4 byte FLOAT data
-----------------------------------------------------------------------
dcar _PDF_
---------- dcar (draw graph for the car file) Ver.0.04 ---------------
usage: dcar input-file (bit-file) (nc)
input-file : car2 file name/text file name(txt|1D|GRD|RF|rtc)/fid file name
bit-file : bit file name
nc : number of the channels to be shown
ex) $>dcar 121212_12.car<RET>
$>dcar 121212_12.car respir.peak.bit 3<RET>
Key control:
Up arrow: Move one page up(channel shift)
Down arrow: Move one page down(channel shift)
Left arrow: Move one page backward(90% shift)
Right arrow: Move one page forward(90% shift)
4: Move the cursor backward(1 pixel step)
6: Move the cursor forward(1 pixel step)
7: Move the cursor backward
9: Move the cursor forward
5: Output the current cursor position
0: Output the values at the current cursor position
a: Autoscale mode(as1/as2/off)
.: Overlay mode(on/off)
b: Verbose mode(on/off)
M: Marker mode(on/off)
m: Set milestone
r: Retrieve milestone
space: Put/Delete the marker
0: Clear all markers
1: Move the cursor to the previous marker
3: Move the cursor to the next marker
+: Toggle the value display modes
o: Save the bit file
s: Save the selected time range as a file
p: Toggle the point display modes
>: Increase the line width or the point size
<: Decrease the line width or the point size
q: Quit the program
-----------------------------------------------------------------------
Compiled [Feb 21 10:09:43 2017] Edited [Nov 9 11:56:16 2016]
dcc_fid
##################################################
# Remove DC atrifact [ver.1.3] 12.Aug.2010 #
##################################################
This program removes dc-artifact from fid file.
Usage: dcc_fid
Output data is float type.(short,int,float>>float)
height: applied for both sides
dc-correction-height: applied for both sides
dc-correction-width: applied for both sides
File Header(32byte):
int nblocks; //# blocks in fid
int ntraces; //# traces per block
int np; //# points per trace
int ebytes; //# bytes per point
int tbytes; //# bytes per trace
int bbytes; //# bytes per block
short transf; //transposed storage flag (not used)
short status; //status of whole file (not used)
int spare1; //reserved for future use (not used)
Block Header(28byte):
short scale; //scaling factor (not used)
short status; //status of data in block (not used)
short index; //block index (not used)
short mode; //mode of data in block (not used)
int ctcount; //ct value for FID (not used)
float lpval; //f2 (2D-f1) left phase in phasefile (not used)
float rpval; //f2 (2D-f1) right phase in phasefile (not used)
float lvl; //level drift correction (not used)
float tlt; //tilt drift correction (not used)
dcc
---------- DCC program Ver.0.1[30.Mar.2009] --------
usage: dcc input_file_name output_file_name (-t) np hight number_of_points number_of_lines
input-file : 4 byte FLOAT data
output-file : 4 byte FLOAT data
-t : optional, Show k-space selection for DCC
np : np(number of data in a readout line)
hight : hight unit definition for dcc
number_of_points : how many points for dcc at left or right
number_of_lines : how many lines for dcc at top and bottom
dcc test.dfid testdcc.dfid 256 64 12 32
-----------------------------------------------------------------------
Compiled [Jul 27 16:40:32 2015] Edited [Jul 27 16:40:23 2015]
dcm2sdt
======== DICOM > sdt/spr data converter Ver.0.1 ========
dcm2sdt<RET> : show this usage
dcm2sdt test.dcm <RET> : convert to sdt/spr
dcm2sdt test.dcm - <RET> : convert to sdt/spr and make CSA files
Compiled [Mar 31 15:43:52 2017] Edited [Mar 31 15:23:49 2017]
dcmall
DICOM -> SDT conversion for all of the folders...
No data folder was found. Abort!
dcmhd
======== DICOM header dump program Ver.2.1 ========
dcmhd<RET> : show this usage
dcmhd test.dcm <RET> : show header information
dcmhd test.dcm 00080008 <RET> : remove the parameter from the DICOM file.
Compiled [Mar 31 15:23:56 2017] Edited [Mar 31 15:03:54 2017]
dcmlog
...Saved dicom data check script[ver.0.0]...
None of 0001_00.dcm nor 0001.dcm can be found. Abort.
dcms2gtb
dcms2sdt
dcms2sdt ver. 0.02c [24.Aug.2016]
Usage: dcm2sdt
>dcms2sdt 0001<RET>
>dcms2sdt . <RET>
If '-' flag is set, skip sdt2to4 and demosaic
decycle
---------- Cyclic fluctuation removal program Ver.0.02 [27.May.2013] --------
Using moving average method
usage: decycle input_file_name nov width (step)<RET>
input-file : 4byte float data
nov : size in the first dimension
width : volume number width for the cycle to be removed(
Applying the process for the first dimension.
ex) $>>decycle test.sdt 2000 4<RET>
-----------------------------------------------------------------------
dedrift2
---------- Slow drift removal program Ver.0.04 ------------------------
Using moving average method
usage: dedrift input_file_name nov width_for_ave [-]<RET>
input-file : 4byte float data (real or complex[-])
nov : size in the first dimension
width_for_ave : width for the moving average(
ex) $>>dedrift test.sdt 100 12<RET>
-----------------------------------------------------------------------
Compiled [Nov 14 17:05:10 2014] Edited [Nov 14 17:04:00 2014]
dedrift3b
---------- Slow drift removal program(for Cyclic data) Ver.0.02 ------------------------
Using moving average method
usage: dedrift3 input_file_name nov width_for_ave [-/+]<RET>
input-file : 4byte float data (real or complex[-/+])
nov : size in the first dimension
width_for_ave : width for the moving average(factor[0~1] or number of samples[1~nov], default: nov/6)
+ : Minus value truncation for the amplitude
Applying the process for the first dimension.
ex) $>>dedrift test.sdt 100 12<RET>
---------------------------------------------------------------------------------------
Compiled [Mar 9 11:58:57 2015] Edited [Mar 9 11:58:20 2015]
dedrift3
---------- Slow drift removal program(for Cyclic data) Ver.0.01 ------------------------
Using moving average method
usage: dedrift3 input_file_name nov width_for_ave [-/+]<RET>
input-file : 4byte float data (real or complex[-/+])
nov : size in the first dimension
width_for_ave : width for the moving average(
Applying the process for the first dimension.
ex) $>>dedrift test.sdt 100 12<RET>
---------------------------------------------------------------------------------------
Compiled [Jan 30 10:19:23 2015] Edited [Jan 30 10:19:09 2015]
dedrift
---------- Slow drift removal program Ver.0.01b [21.May.2013] --------
Using moving average method
usage: dedrift input_file_name nov width_for_ave [-]<RET>
input-file : 4byte float data (real or complex[-])
nov : size in the first dimension
width_for_ave : width for the moving average(
ex) $>>dedrift test.sdt 12 100<RET>
-----------------------------------------------------------------------
deface
usage: mri_deface
degibbs002_tst
---------- degibbs (avoid Gibbs ringing) Ver.0.0.1tst 2012.Aug.15--------
usage: degibbs [input_fname_body] (threshold) (edge) (smooth) (-)
[input_fname_body].edt/epr are used as the input.
Output file name: [input_fname_body]-dG.edt/epr
threshold : threshold(%,default:0.1)
edge : edge width(%,default:4)
smooth : smoothing factor(default:32)
- : For 2D data set
The output file has float type data.
$>degibbs mprage01<RET>
-----------------------------------------------------------------
degibbs002
---------- degibbs (avoid Gibbs ringing) Ver.0.0.2 2012.Aug.15--------
usage: degibbs [input_fname_body] (-)
[input_fname_body].edt/epr are used as the input.
Output file name: [input_fname_body]-dG.edt/epr
- : For 2D data set
The output file has float type data.
$>degibbs mprage01<RET>
-----------------------------------------------------------------
degibbs003_tst
---------- degibbs (avoid Gibbs ringing) Ver.0.0.3tst 2012.Aug.28--------
usage: degibbs [input_fname_body] (threshold) (edge) (smooth) (gamma) (-)
[input_fname_body].edt/epr are used as the input.
Output file name: [input_fname_body]-dG.edt/epr
threshold : threshold(%,default:0.1)
edge : edge width(%,default:4)
smooth : smoothing factor(default:32)
gamma : gammma value for the mask normalization(default:5)
- : For 2D data set
The output file has float type data.
$>degibbs mprage01<RET>
-----------------------------------------------------------------
degibbs
---------- degibbs (avoid Gibbs ringing) Ver.0.0.1 2012.Feb.24--------
usage: degibbs [input_fname_body] (-)
[input_fname_body].edt/epr are used as the input.
Output file name: [input_fname_body]-dG.edt/epr
- : For 2D data set
The output file has float type data.
$>degibbs mprage01<RET>
-----------------------------------------------------------------
demosaic
demosaic ver. 0.1 [9.Oct.2015]
demosaic [file name body] (x) (y) (s)<RET>
You should have [file name body].sdt/spr
(x) (y) (s) : true matrix size(non-mosaic)
You can ommit (xy) or (s).
>demosaic run1 64 64 20<RET>
>demosaic run1 64 64<RET>
>demosaic run1 20<RET>
>demosaic run1 <RET>
despike_tst
despike +dedrift v0.00
********************************************************************
despike+dedrift for the temporal time course on sdt/spr files
Usage: despike Input_filenamebody (despike_flag) (dedrift_flag)
Only float type sdt/spr files are supported.
despike_flag: MAD scale factor (default as 6.8)
despike_flag: percentage for averaging (default as 17)
EX) If you have
despike data<RET>
despike data 4 15<RET>
********************************************************************
Compiled [Sep 16 14:48:04 2016] Edited [Sep 16 14:50:02 2016]
despike
despike v0.00
********************************************************************
despike for the temporal time course on sdt/spr files
Usage: despike Input_filenamebody (filter_size)
Only float type sdt/spr files are supported.
EX) If you have
despike data<RET>
********************************************************************
Compiled [May 26 09:42:24 2016] Edited [May 26 09:42:21 2016]
detrend
----- Spatial Detrend ver. 0.01 [16.Mar.2010] -----
>>detrend [filename_body] (FWHM factor1 factor2)<RET>
default value: (FWHM factor1 factor2) = (20 -0.5 4)
FWHM -- FWHM of spatial gaussian filter for trend map calculation
factor1 -- Threshold factor for masking (threshold = ave - factor1 * sdv)
factor2 -- Scale factor for value padding (factor2 * threshold)
ex.) [for 3d.t1.sdt/spr]
$>detrend 3d.t1<RET>
$>detrend 3d.t1 30 0 5<RET>
-----------------------------------------
dgb
DIR: /Users/kenji/scripts/macbin
dgraph
---------- dgraph (draw graph for the data in ascii file) Ver.0.00[16.Feb.2013] --------
usage: dgraph input-file (ng) (-)
input-file : ascii data
ng : number of graph
- : Transpose the data matrix
ex) dgraph asc.txt 3
-----------------------------------------------------------------------
dgrd0
-------- GRD waveform display program 0.0(2011.Feb.14) --------
$>dgrd file1.GRD<RET>
$>dgrd file1.GRD file2.GRD<RET>
When you want to see the points, put "-" at the end of the command
$>dgrd file1.GRD file2.GRD -<RET>
dgrd
-------- GRD waveform display program 0.1(2012.Aug.7) --------
$>dgrd file1.GRD<RET>
$>dgrd file1.GRD file2.GRD<RET>
When you want to see the points, put "-" at the end of the command
$>dgrd file1.GRD file2.GRD -<RET>
dgs001
dgs ver. 0.01 [31.Aug.2016]
dgs
dgs
dgs ver. 0.00 [13.Jul.2016]
dgs
dg
----- Show parameters from fid ver. 1.4g [20.Mar.2014] -----
>>dg [filename]<RET>
ex.) [for anat.fid]
$>dg anat(.fid)<RET>
$>dg anat(.fid) + <RET> /* additional info */
-----------------------------------------
dif
dif v0.00
********************************************************************
Make 1st order derivative models
Usage: dif model_file<RET>
********************************************************************
Compiled [May 24 11:23:38 2017] Edited [May 24 10:55:42 2017]
dilate_vmr
---------- dilate volume program for vmr Ver.0.2[24.Jul.2012] --------
usage: dilate_vmr [input vmr filename] [output vmr filename] [mark_color_target] [mark_color_new] [radius]
-----------------------------------------------------------------------
diochk
dyld: Library not loaded: /Library/Frameworks/nidaqmxbase.framework/Versions/3/nidaqmxbase
Referenced from: /usr4/local/mac_bin2/diochk
Reason: image not found
dip3d _PDF_
dip3d v0.00
********************************************************************
Usage: dip3d sdt_filebody (threshold) (steps)<RET>
sdt_filebody: sdt/spr filename body
output:
********************************************************************
Compiled [Mar 9 16:40:54 2018] Edited [Mar 9 16:48:19 2018]
diskw
>>>>> WRITE PERFORMANCE TEST <<<<<
6400+0 records in
6400+0 records out
838860800 bytes transferred in 0.793465 secs (1057212236 bytes/sec)
6400+0 records in
6400+0 records out
838860800 bytes transferred in 0.797587 secs (1051748444 bytes/sec)
6400+0 records in
6400+0 records out
838860800 bytes transferred in 0.819433 secs (1023708865 bytes/sec)
6400+0 records in
6400+0 records out
838860800 bytes transferred in 0.820283 secs (1022648117 bytes/sec)
6400+0 records in
6400+0 records out
838860800 bytes transferred in 0.799487 secs (1049248681 bytes/sec)
6400+0 records in
6400+0 records out
838860800 bytes transferred in 0.790634 secs (1060997741 bytes/sec)
6400+0 records in
6400+0 records out
838860800 bytes transferred in 0.792060 secs (1059087579 bytes/sec)
6400+0 records in
6400+0 records out
838860800 bytes transferred in 0.794784 secs (1055457492 bytes/sec)
6400+0 records in
6400+0 records out
838860800 bytes transferred in 0.803086 secs (1044546606 bytes/sec)
6400+0 records in
6400+0 records out
838860800 bytes transferred in 0.798328 secs (1050771901 bytes/sec)
dotpng _PDF_ _SAMPLE_
----- USAGE: dotpng (random dot png creator) ------------
> dotpng filenamebody width height ndots [nframe lifetime speed mask1 mask2 (motionflag)]<RET>
optional(dotpattern): dotpat.txt
e.g.)
>dotpng dots0 800 600 1000 20 10 2 40 300 <RET>
>dotpng dots0 800 600 500 <RET>
----------------------------------------------------------
Compiled [Jul 28 08:59:41 2021] Edited [Jul 28 08:59:38 2021]
dots
---------- Create random dots as 1byte data Ver.0.0 --------
usage: dots output_file_name_body x y ndot (dsize)
output-file : 1 byte int data(sdt/spr)
x : matrix size in horizontal direction
y : matrix size in vertical direction
ndot : number of dots
dsize : dot size as radius(pixels)
'srand()' and 'rand()' funtions are used.
rand()'s RANGE: 0 - 2147483647
Output data = amp x (rand()/RAND_MAX - 0.5) + ave
--------------------------------------------------------------------
Compiled [May 8 11:46:30 2017] Edited [May 8 11:18:30 2017]
dpe
-------- Display petable visually 0.1(2015.Jan.27) --------
$>dpe petable_file<RET>
$>dpe epi128lin2k<RET>
dprocp
----- Show parameter from procpar ver. 1.1 [15.Jan.2010] -----
>>dprocp [filename_body]<RET>
ex.) [for anat.fid/procpar]
$>dprocp anat pss
-----------------------------------------
dsort
---------- Float data sorting program Ver.0.00[10.Oct.2013] --------
usage: dsort input_file_name output_file_name [-]
input-file : 4 byte FLOAT data
output-file : 4 byte Float data (ascending order:default)
-: reverse the sort order(descending order)
-----------------------------------------------------------------------
dtipp2
----- dtipp ver. 0.01 [11.Mar.2014] -----
DTI data postprocessing tool
>>dtipp ../raw/dti01<RET>
>>dtipp ../raw/dti01 -<RET>
The processed data will appear in the current directory
'-' flag is for displaying the data with view2d
-----------------------------------------
dtipp
----- dtipp ver. 0.00 [3.Mar.2014] -----
DTI data postprocessing tool
>>dtipp ../raw/dti01<RET>
>>dtipp ../raw/dti01 -<RET>
The processed data will appear in the current directory
'-' flag is for displaying the data with view2d
-----------------------------------------
edge
---------- Edge enhancement program Ver.0.00 --------
usage: edge file_name_body
input-file : [file_name_body].sdt/spr
output-file : [file_name_body]_edge?.sdt/spr
-------------------------------------------------
Compiled [Feb 27 17:47:20 2014] Edited [Feb 27 17:47:06 2014]
eflipedt
------- eflipedt -------
eflipedt ver. 1.1b [16.Mar.2010]
eflipedt
You should have [file name body].edt/epr
eflipfid
###############################################################
# Endian flip for Fid data [ver.1.1a] 30.Aug.2010 #
###############################################################
This program does endianflip for fid data.
Usage: eflipfid
The fid data will be overwritten.
File Header(32byte):
int nblocks; //# blocks in fid
int ntraces; //# traces per block
int np; //# points per trace
int ebytes; //# bytes per point
int tbytes; //# bytes per trace
int bbytes; //# bytes per block
short transf; //transposed storage flag (not used)
short status; //status of whole file (not used)
int spare1; //reserved for future use (not used)
Block Header(28byte):
short scale; //scaling factor (not used)
short status; //status of data in block (not used)
short index; //block index (not used)
short mode; //mode of data in block (not used)
int ctcount; //ct value for FID (not used)
float lpval; //f2 (2D-f1) left phase in phasefile (not used)
float rpval; //f2 (2D-f1) right phase in phasefile (not used)
float lvl; //level drift correction (not used)
float tlt; //tilt drift correction (not used)
eflipnii
-----niiflt (version 0.0) ----
For NIFTI data type conversion
usage: niiflt test.nii<RET>
--------------------------------------------------
Compiled [Mar 13 11:28:30 2017] Edited [Mar 13 11:11:05 2017]
eflipsdt
------- eflipsdt -------
eflipsdt ver. 1.2 [8.Jun.2011]
eflipsdt
You should have [file name body].sdt/spr or .edt/epr
eflip
----- eflip [endian flip] Mar.14.2008 -----
eflip [filename] [byte number]<RET>
byte number: 2 or 4 or 8
eight2four
---------- Long Int(8)>Float(4) conversion program Ver.0.1[9.Aug.2010] --------
usage: eight2four input_file_name output_file_name
input-file : 8 byte Long INT data
output-file : 4 byte FLOAT data
-----------------------------------------------------------------------
endianflip
---------- endian flipping program Ver.0.13[19.Jun.2012] --------
usage: endianflip input_file_name output_file_name (number_of_byte)
input-file : 8 or 4(default) or 2 byte data
output-file : 8 or 4 ro 2 byte data
-----------------------------------------------------------------------
endian
LITTLE
epibsi6.15
USAGE: epibsi6 Input_file [Mag_cor Phase_cor DC_cor Print_nav_echo_data Slice_# Sout (-)]
Ver.6.15 [11-15-2011]
Mag_cor: controls whether the navigator echo magnitude is used to correct amplitudes between segments. Default 1 (=YES)
Phase_cor: controls whether the navigator echo is used to adjust the phase between segments. Default 1 (=YES) for 2D, Default 0 (=NO) for 3D
DC_cor: controls whether DC correction is done on the echos. Default 0 (=NO)
0: no 1: correction line by line 2:by shot 3:by slice 4:by volume 5:by all
Print_nav_echo_data: controls whether a navigator echo file is written out. Default 0 (=NO)
Slice#: is the slice from which the navigator echo info is written out. Default 1 (=slice number 1) [*Set -1 to skip reference scan correction]
Sout : is for short integer output; the maximum value for normalization. If 0, normalized by its max. Default: -1 is for float data output.
- : is set to apply single navigator echo correction for 3 line navigator echo data
epibsi6.19j
USAGE: epibsi6 Input_file [Mag_cor Phase_cor DC_cor Print_nav_echo_data Slice_# Sout (-)]
Ver.6.19j [2-8-2013]
Mag_cor: controls whether the navigator echo magnitude is used to correct amplitudes between segments. Default 1 (=YES)
Phase_cor: controls whether the navigator echo is used to adjust the phase between segments. Default 1 (=YES) for 2D, Default 0 (=NO) for 3D
DC_cor: controls whether DC correction is done on the echos. Default 0 (=NO)
0: no 1: correction line by line 2:by shot 3:by slice 4:by volume 5:by all
Print_nav_echo_data: controls whether a navigator echo file is written out. Default 0 (=NO)
Slice#: is the slice from which the navigator echo info is written out. Default 1 (=slice number 1) [*Set -1 to skip reference scan correction]
Sout : is for short integer output; the maximum value for normalization. If 0, normalized by its max. Default: -1 is for float data output.
- : is set to apply single navigator echo correction for 3 line navigator echo data
epibsi6.1
USAGE: epibsi6 Input_file [Mag_cor Phase_cor DC_cor Print_nav_echo_data Slice_# Sout (-)]
Ver.6.19j [2-8-2013]
Mag_cor: controls whether the navigator echo magnitude is used to correct amplitudes between segments. Default 1 (=YES)
Phase_cor: controls whether the navigator echo is used to adjust the phase between segments. Default 1 (=YES) for 2D, Default 0 (=NO) for 3D
DC_cor: controls whether DC correction is done on the echos. Default 0 (=NO)
0: no 1: correction line by line 2:by shot 3:by slice 4:by volume 5:by all
Print_nav_echo_data: controls whether a navigator echo file is written out. Default 0 (=NO)
Slice#: is the slice from which the navigator echo info is written out. Default 1 (=slice number 1) [*Set -1 to skip reference scan correction]
Sout : is for short integer output; the maximum value for normalization. If 0, normalized by its max. Default: -1 is for float data output.
- : is set to apply single navigator echo correction for 3 line navigator echo data
epibsi6
USAGE: epibsi6 Input_file [Mag_cor Phase_cor DC_cor Print_nav_echo_data Slice_# Sout (-)]
Ver.6.19j [2-8-2013]
Mag_cor: controls whether the navigator echo magnitude is used to correct amplitudes between segments. Default 1 (=YES)
Phase_cor: controls whether the navigator echo is used to adjust the phase between segments. Default 1 (=YES) for 2D, Default 0 (=NO) for 3D
DC_cor: controls whether DC correction is done on the echos. Default 0 (=NO)
0: no 1: correction line by line 2:by shot 3:by slice 4:by volume 5:by all
Print_nav_echo_data: controls whether a navigator echo file is written out. Default 0 (=NO)
Slice#: is the slice from which the navigator echo info is written out. Default 1 (=slice number 1) [*Set -1 to skip reference scan correction]
Sout : is for short integer output; the maximum value for normalization. If 0, normalized by its max. Default: -1 is for float data output.
- : is set to apply single navigator echo correction for 3 line navigator echo data
epibsi
USAGE: epibsi6 Input_file [Mag_cor Phase_cor DC_cor Print_nav_echo_data Slice_# Sout (-)]
Ver.6.19j [2-8-2013]
Mag_cor: controls whether the navigator echo magnitude is used to correct amplitudes between segments. Default 1 (=YES)
Phase_cor: controls whether the navigator echo is used to adjust the phase between segments. Default 1 (=YES) for 2D, Default 0 (=NO) for 3D
DC_cor: controls whether DC correction is done on the echos. Default 0 (=NO)
0: no 1: correction line by line 2:by shot 3:by slice 4:by volume 5:by all
Print_nav_echo_data: controls whether a navigator echo file is written out. Default 0 (=NO)
Slice#: is the slice from which the navigator echo info is written out. Default 1 (=slice number 1) [*Set -1 to skip reference scan correction]
Sout : is for short integer output; the maximum value for normalization. If 0, normalized by its max. Default: -1 is for float data output.
- : is set to apply single navigator echo correction for 3 line navigator echo data
epipp
----- epipp ver. 0.02 [2.Dec.2012] -----
epi data postprocessing tool
>>epipp ../raw/epi01<RET>
>>epipp ../raw/epi01 -<RET>
The processed data will appear in the current directory
'-' flag is for displaying the data with view2d
-----------------------------------------
euler2trm
---------- Make TRM from Euler angles Ver.0.00[21.Feb.2011] --------
usage: euler2trm psi phi theta (-/-FDF) <RET>
x1 x2 x3
y1 y2 y3
z1 z2 z3
The transformation matrix is adjusted for NIFTI(AFNI View)
- : TRM for monkey data
-FDF: make output for orientation parameter of fdf file
-----------------------------------------------------------------------
ext_analyzer _PDF_
##########################################################
# Analog data (.ext/.alg/.car) processing tool v1.0.5 #
##########################################################
Usage: ext_analyzer FILENAME (threshold)
threshold: -5~5 [default=2.5]
Example:
$> ext_analyzer 031023.ext<RET>
$> ext_analyzer 031023.ext -1<RET>
Compiled [Aug 17 11:56:18 2016] Edited [Aug 17 11:57:57 2016]
fdf2sdt
----- fdf2sdt ver. 1.1 [11.Aug.2011] -----
>>fdf2sdt [fdf_filename/fdf_foldername] ([output_filenamebody]) <RET>
>>fdf2sdt test.fdf<RET>
Output: test.sdt/spr
>>fdf2sdt test.fdf new<RET>
Output: new.sdt/spr
>>fdf2sdt gemsir.img new<RET>
Output: new.sdt/spr
-----------------------------------------
fdfh2spr
----- fidh2spr ver. 1.1b [12.Jul.2011] -----
>>fidh2spr [fdfh_filename] [spr_filename]<RET>
-----------------------------------------
fdf_head
#########################################################
# fdf_head RIKEN_BSI ver.0.0 Feb.16.2012 #
#########################################################
USAGE: fdf_head [inputfdf_file]<RET>
Example:
$> fdf_head data.fdf<RET>
fdfsplit
#########################################################
# fdfsplit RIKEN_BSI ver.0.0 Jun.28.2011 #
#########################################################
USAGE: fdfsplit [inputfdf_file] data_file header_file
Example:
$> fdfsplit data.fdf data head<RET>
fdrp _PDF_
fdrp v0.00
********************************************************************
fdr thresholding program
Usage: fdrp
pval_file: float binary file(pvalue)
q_threshold: q_value threshold (0.05 as default)
method:
1(default): Benjamini and Hochberg 1995
********************************************************************
Compiled [Apr 21 10:39:41 2017] Edited [Apr 21 10:15:05 2017]
fftcomplex
The number of processors is 8
The number of threads is 3
##################################################
# 3d fft complex for 4d data [ver.1.8b] #
##################################################
This program does 3dfft for 4d data(for float data)
Usage: fftcomplex
Usage: fftcomplex
dim1: 1st dimension(3dfft)
dim2: 2nd dimension(3dfft)
dim3: 3rd dimension(3dfft)
dim4: 4th dimension(No fft)
offset#: voxel offset value ratio(0.5 for half fov) for individual axis(1-3).
The data file size should be eual to (dim1xdim2xdim3xdim4) x 8 .
-re : output real data(without fft)
-im : output imaginary data(without fft)
-sq : output square of magnitude data(without fft)
-mg : output magnitude data(without fft)
-ph : output phase data(without fft)
-ft : output the complex data(without fft) as edt
-fre : output real data(with fft)
-fim : output imaginary data(with fft)
-fsq : output square of magnitude data(with fft)
-fmg : output magnitude data(with fft:default)
-fph : output phase data(with fft)
-fft : output data(with fft) as edt
---
Compiled [Jan 20 15:31:08 2015] Edited [Jan 20 15:13:16 2015]
fftreal
The number of processors is 8
The number of threads is 3
##############################################
# 3d fft for 4d real data [ver.0.0] #
##############################################
This program does 3dfft for 4d real data(for float data)
Usage: fftreal
Usage: fftreal
dim1: 1st dimension(3dfft)
dim2: 2nd dimension(3dfft)
dim3: 3rd dimension(3dfft)
dim4: 4th dimension(No fft)
offset#: voxel offset value ratio(0.5 for half fov) for individual axis(1-3).
The data file size should be eual to (dim1xdim2xdim3xdim4) x 8 .
-re : output real data(without fft)
-im : output imaginary data(without fft)
-sq : output square of magnitude data(without fft)
-mg : output magnitude data(without fft)
-ph : output phase data(without fft)
-ft : output the complex data(without fft) as edt
-fre : output real data(with fft)
-fim : output imaginary data(with fft)
-fsq : output square of magnitude data(with fft)
-fmg : output magnitude data(with fft:default)
-fph : output phase data(with fft)
-fft : output data(with fft) as edt
---
Compiled [May 27 17:36:22 2016] Edited [May 27 17:36:20 2016]
fftw3d_2
----- fftw3d ver. 2.0 [9.Mar.2010] -----
>>fftw3d [filename_body] (butterworth_order) (butterworth_radius) (DC_correction)<RET>
ex.) [for 3d.fid/fid,procpar <4byte int complex>]
$>fftw3d 3d 8
$>fftw3d 3d 16 0.8
$>fftw3d 3d 8 1 0
-----------------------------------------
fftw3d2
----- fftw3d ver. 1.6 [4.Mar.2008] -----
>>fftw3d [filename_body] (butterworth_order) (butterworth_radius)<RET>
ex.) [for 3d.fid/fid,procpar <4byte int complex>]
$>fftw3d 3d 8
$>fftw3d 3d 16 0.8
-----------------------------------------
fftw3dexe
dyld: Library not loaded: /sw/lib/libfftw3.3.dylib
Referenced from: /usr4/local/mac_bin2/fftw3dexe
Reason: image not found
fftw3d
----- fftw3d ver. 1.8 [14.Apr.2009] -----
>>fftw3d [filename_body] (butterworth_order) (butterworth_radius) (DC_correction)<RET>
ex.) [for 3d.fid/fid,procpar <4byte int complex>]
$>fftw3d 3d 8
$>fftw3d 3d 16 0.8
$>fftw3d 3d 8 1 0
-----------------------------------------
fid2edt132
############################################################
# convert *.fid to *.edt [ver.1.32] 12.Oct.2011 #
############################################################
Usage: fid2edt
input data: 32-bit integer, 16-bit integer or 32-bit float complex
output data: Same as input data
File Header(32byte):
int nblocks; //# blocks in fid
int ntraces; //# traces per block
int np; //# points per trace
int ebytes; //# bytes per point
int tbytes; //# bytes per trace
int bbytes; //# bytes per block
short transf; //transposed storage flag (not used)
short status; //status of whole file (not used)
int spare1; //reserved for future use (not used)
Block Header(28byte):
short scale; //scaling factor (not used)
short status; //status of data in block (not used)
short index; //block index (not used)
short mode; //mode of data in block (not used)
int ctcount; //ct value for FID (not used)
float lpval; //f2 (2D-f1) left phase in phasefile (not used)
float rpval; //f2 (2D-f1) right phase in phasefile (not used)
float lvl; //level drift correction (not used)
float tlt; //tilt drift correction (not used)
fid2edt
############################################################
# convert *.fid to *.edt [ver.1.34] 8.Mar.2013 #
############################################################
Usage: fid2edt
input data: 32-bit integer, 16-bit integer or 32-bit float complex
output data: Same as input data(default)
flag
-:output as cpu endian
-f:float output(cpu endian)
File Header(32byte):
int nblocks; //# blocks in fid
int ntraces; //# traces per block
int np; //# points per trace
int ebytes; //# bytes per point
int tbytes; //# bytes per trace
int bbytes; //# bytes per block
short transf; //transposed storage flag (not used)
short status; //status of whole file (not used)
int spare1; //reserved for future use (not used)
Block Header(28byte):
short scale; //scaling factor (not used)
short status; //status of data in block (not used)
short index; //block index (not used)
short mode; //mode of data in block (not used)
int ctcount; //ct value for FID (not used)
float lpval; //f2 (2D-f1) left phase in phasefile (not used)
float rpval; //f2 (2D-f1) right phase in phasefile (not used)
float lvl; //level drift correction (not used)
float tlt; //tilt drift correction (not used)
fid2hdr_1.0
DATATYPE: UNKNOWN, BINARY,CHAR, SHORT, INT, FLOAT, COMPLEX, DOUBLE, RGB
---- fid2hdr ver 1.0i 2010.3.4 ----
usage: fid2hdr fidname niftiname
usage: fid2hdr fidname niftiname DATATYPE
fid2hdr3
DATATYPE: UNKNOWN, BINARY,CHAR, SHORT, INT, FLOAT(default), COMPLEX, DOUBLE, RGB
---- fid2hdr ver 3.1 2012.2.21 ----
usage: fid2hdr fidname niftiname (DATATYPE) (MONKEY_FLAG)
MONKEY_FLAG: -M
e.g.) for mprage.fid
$>fid2hdr mprage mprage.hdr<RET>
$>fid2hdr mprage mprage.hdr SHORT -M<RET>
fid2hdr_flip
DATATYPE: UNKNOWN, BINARY,CHAR, SHORT, INT, FLOAT, COMPLEX, DOUBLE, RGB
---- fid2hdr ver 1.0k testing 2010.4.7 ----
usage: fid2hdr fidname niftiname
usage: fid2hdr fidname niftiname DATATYPE
fid2hdr
DATATYPE: UNKNOWN, BINARY,CHAR, SHORT, INT, FLOAT(default), COMPLEX, DOUBLE, RGB
---- fid2hdr ver 2.0 2011.11.17 ----
usage: fid2hdr fidname niftiname
usage: fid2hdr fidname niftiname DATATYPE
fid2sdt_004
----- fid2sdt ver. 0.04 [17.Nov.2011] -----
fid data conversion to sdt/spr
$>fid2sdt anat3d.fid<RET>
$>fid2sdt anat2d.fid<RET>
-----------------------------------------
fid2sdt_005
----- fid2sdt ver. 0.05c [8.Feb.2012] -----
fid data conversion to sdt/spr
$>fid2sdt anat3d.fid<RET>
$>fid2sdt anat2d.fid<RET>
-----------------------------------------
fid2sdt_007
----- fid2sdt ver. 0.07 [23.Feb.2012] -----
fid data conversion to sdt/spr
Usage: $>fid2sdt fid_foldername (sdt_filename_body) (-)<RET>
-: This flag is for degibbs(gibbs ringing removal)
$>fid2sdt anat3d.fid<RET>
$>fid2sdt anat2d.fid test - <RET>
-----------------------------------------
fid2sdt_011
----- fid2sdt ver. 0.1.1 [17.Sep.2012] -----
fid data conversion to sdt/spr
Usage: $>fid2sdt fid_foldername (sdt_filename_body) (xfrac yfrac zfrac) (-/+)<RET>
xfrac yfrac zfrac: fraction for zerofilling. 1 is default for no-filling)
-: This flag is for degibbs(gibbs ringing removal)
+: This flag is for k-space magnitude data output
$>fid2sdt anat3d.fid<RET>
$>fid2sdt anat2d.fid test - <RET>
-----------------------------------------
fid2sdt_012
----- fid2sdt ver. 0.1.2 [17.Dec.2012] -----
fid data conversion to sdt/spr
Usage: $>fid2sdt fid_foldername (sdt_filename_body) (xfrac yfrac zfrac) (-/+)<RET>
xfrac yfrac zfrac: fraction for zerofilling. 1 is default for no-filling)
-: This flag is for degibbs(gibbs ringing removal)
+: This flag is for k-space magnitude data output
$>fid2sdt anat3d.fid<RET>
$>fid2sdt anat2d.fid test - <RET>
-----------------------------------------
fid2sdt017
----- fid2sdt ver. 0.1.7b [4.Sep.2014] -----
fid data conversion to sdt/spr
Usage: $>fid2sdt fid_foldername (sdt_filename_body) (xfrac yfrac zfrac) (-/+)<RET>
xfrac yfrac zfrac: fraction for zerofilling. 1 is default for no-filling)
-: This flag is for degibbs(gibbs ringing removal)
+: This flag is for k-space magnitude data output as sdt/spr
++: This flag is for k-space data output as edt/epr
$>fid2sdt anat3d.fid<RET>
$>fid2sdt anat2d.fid test - <RET>
-----------------------------------------
fid2sdt_018
----- fid2sdt ver. 0.1.8 [24.Sep.2015] -----
fid data conversion to sdt/spr
Usage: $>fid2sdt fid_foldername (sdt_filename_body) (xfrac yfrac zfrac) (-/+)<RET>
xfrac yfrac zfrac: fraction for zerofilling. 1 is default for no-filling)
-: This flag is for degibbs(gibbs ringing removal)
+: This flag is for k-space magnitude data output as sdt/spr
++: This flag is for k-space data output as edt/epr
$>fid2sdt anat3d.fid<RET>
$>fid2sdt anat2d.fid test - <RET>
-----------------------------------------
fid2sdt
----- fid2sdt ver. 0.1.5 [18.Oct.2013] -----
fid data conversion to sdt/spr
Usage: $>fid2sdt fid_foldername (sdt_filename_body) (xfrac yfrac zfrac) (-/+)<RET>
xfrac yfrac zfrac: fraction for zerofilling. 1 is default for no-filling)
-: This flag is for degibbs(gibbs ringing removal)
+: This flag is for k-space magnitude data output
$>fid2sdt anat3d.fid<RET>
$>fid2sdt anat2d.fid test - <RET>
-----------------------------------------
fidb2sdt0
scale factor : 1 x 1 x 1
Missing /Users/kenji/scripts/macbin/fid
fidb2sdt
scale factor : 1 x 1 x 1
Missing /Users/kenji/scripts/macbin/fid
fidchk
...Fid data check script[ver.0.0]...
No such file [*.fid.fid/fid]
fid_head
#########################################################
# Show Fid header [ver.1.3d] 3.Jun.2011 #
#########################################################
This program shows the fid header.
Usage: fid_head
File Header(32byte):
int nblocks; //# blocks in fid
int ntraces; //# traces per block
int np; //# points per trace
int ebytes; //# bytes per point
int tbytes; //# bytes per trace
int bbytes; //# bytes per block
short transf; //transposed storage flag (not used)
short status; //status of whole file (not used)
int spare1; //reserved for future use (not used)
Block Header(28byte):
short scale; //scaling factor (not used)
short status; //status of data in block (not used)
short index; //block index (not used)
short mode; //mode of data in block (not used)
int ctcount; //ct value for FID (not used)
float lpval; //f2 (2D-f1) left phase in phasefile (not used)
float rpval; //f2 (2D-f1) right phase in phasefile (not used)
float lvl; //level drift correction (not used)
float tlt; //tilt drift correction (not used)
fidlogb
...Saved data check script...
The directory[./] doesn't have any fid data set.
Check your data folder.
fidlog
...Saved data check script[ver.0.3e]...
...Saved data check script...
The directory[./] doesn't have any fid data set.
Check your data folder.
fid_merge
###############################################################
# Merge Fid header and data into fid [ver.1.12b] 1.Sep.2010 #
###############################################################
This program unify fid header and data into fid.
Usage: fid_merge
When '-' is given, the first block header is used for all blocks.
File Header(32byte):
int nblocks; //# blocks in fid
int ntraces; //# traces per block
int np; //# points per trace
int ebytes; //# bytes per point
int tbytes; //# bytes per trace
int bbytes; //# bytes per block
short transf; //transposed storage flag (not used)
short status; //status of whole file (not used)
int spare1; //reserved for future use (not used)
Block Header(28byte):
short scale; //scaling factor (not used)
short status; //status of data in block (not used)
short index; //block index (not used)
short mode; //mode of data in block (not used)
int ctcount; //ct value for FID (not used)
float lpval; //f2 (2D-f1) left phase in phasefile (not used)
float rpval; //f2 (2D-f1) right phase in phasefile (not used)
float lvl; //level drift correction (not used)
float tlt; //tilt drift correction (not used)
fid_mkhead
#########################################################
# Make Fid header [ver.1.0] 4.Mar.2008 #
#########################################################
This program makes the fid header.
Usage: fid_head
File Header(32byte):
long nblocks; //# blocks in fid
long ntraces; //# traces per block
long np; //# points per trace
long ebytes; //# bytes per point
long tbytes; //# bytes per trace
long bbytes; //# bytes per block
short transf; //transposed storage flag (not used)
short status; //status of whole file (not used)
long spare1; //reserved for future use (not used)
Block Header(28byte):
short scale; //scaling factor (not used)
short status; //status of data in block (not used)
short index; //block index (not used)
short mode; //mode of data in block (not used)
long ctcount; //ct value for FID (not used)
float lpval; //f2 (2D-f1) left phase in phasefile (not used)
float rpval; //f2 (2D-f1) right phase in phasefile (not used)
float lvl; //level drift correction (not used)
float tlt; //tilt drift correction (not used)
fid_shim
####################################################################
# fid data update for multi receive shim [ver.0.3] 30.Oct.2012 #
####################################################################
This program modifies fid data for multi receive shimming.
Usage: fid_shim
File Header(32byte):
int nblocks; //# blocks in fid
int ntraces; //# traces per block
int np; //# points per trace
int ebytes; //# bytes per point
int tbytes; //# bytes per trace
int bbytes; //# bytes per block
short transf; //transposed storage flag (not used)
short status; //status of whole file (not used)
int spare1; //reserved for future use (not used)
Block Header(28byte):
short scale; //scaling factor (not used)
short status; //status of data in block (not used)
short index; //block index (not used)
short mode; //mode of data in block (not used)
int ctcount; //ct value for FID (not used)
float lpval; //f2 (2D-f1) left phase in phasefile (not used)
float rpval; //f2 (2D-f1) right phase in phasefile (not used)
float lvl; //level drift correction (not used)
float tlt; //tilt drift correction (not used)
fid_split
############################################################
# Split Fid into header and data [ver.1.2b] 24.Feb.2012 #
############################################################
This program split fid data into header and data.
Usage: fid_split
File Header(32byte):
int nblocks; //# blocks in fid
int ntraces; //# traces per block
int np; //# points per trace
int ebytes; //# bytes per point
int tbytes; //# bytes per trace
int bbytes; //# bytes per block
short transf; //transposed storage flag (not used)
short status; //status of whole file (not used)
int spare1; //reserved for future use (not used)
Block Header(28byte):
short scale; //scaling factor (not used)
short status; //status of data in block (not used)
short index; //block index (not used)
short mode; //mode of data in block (not used)
int ctcount; //ct value for FID (not used)
float lpval; //f2 (2D-f1) left phase in phasefile (not used)
float rpval; //f2 (2D-f1) right phase in phasefile (not used)
float lvl; //level drift correction (not used)
float tlt; //tilt drift correction (not used)
fidstat
######################################################
# Display the Statistics of Fid data [ver.0.1f] #
######################################################
This program shows the statistics on fid data.
Usage: fidstat
Usage: fidstat
Compiled [Nov 8 16:31:33 2013] Edited [Nov 8 16:31:25 2013]
fidtstb
############################################################
# Fid data check program [ver.0.0] 17.Feb.2016 #
############################################################
This program checks your fid data.
Usage: fidbtst
length_threshold: the number thredhold of consecutive data(default:5)
fidtst
############################################################
# Fid data check program [ver.0.7] 18.Jul.2012 #
############################################################
This program checks your fid data.
Usage: fidtst
length_threshold: the number thredhold of consecutive data(default:5)
File Header(32byte):
int nblocks; //# blocks in fid
int ntraces; //# traces per block
int np; //# points per trace
int ebytes; //# bytes per point
int tbytes; //# bytes per trace
int bbytes; //# bytes per block
short transf; //transposed storage flag (not used)
short status; //status of whole file (not used)
int spare1; //reserved for future use (not used)
Block Header(28byte):
short scale; //scaling factor (not used)
short status; //status of data in block (not used)
short index; //block index (not used)
short mode; //mode of data in block (not used)
int ctcount; //ct value for FID (not used)
float lpval; //f2 (2D-f1) left phase in phasefile (not used)
float rpval; //f2 (2D-f1) right phase in phasefile (not used)
float lvl; //level drift correction (not used)
float tlt; //tilt drift correction (not used)
filt33
The number of processors is 8
filt33 v0.00
********************************************************************
2D 3x3 convolution filter application on sdt/spr files
Usage: filt33 Input_filenamebody filterfile33
filt33 Input_filenamebody filtvalue1 filtvalue2 filtvalue3 ...filtvalue9
filterfile33: 3x3 filter file(text)
filtval(n) : 3x3 filter values
EX) If you have
filt33 data<RET>
filt33 data laplace.txt<RET>
********************************************************************
Compiled [Mar 13 14:14:47 2014] Edited [Mar 13 14:14:34 2014]
filt55
The number of processors is 8
filt55 v0.00
********************************************************************
2D 5x5 convolution filter application on sdt/spr files
Usage: filt55 Input_filenamebody filterfile55
filt55 Input_filenamebody filtvalue1 filtvalue2 filtvalue3 ...filtvalue25
filterfile55: 5x5 filter file(text)
filtval(n) : 5x5 filter values
EX) If you have
filt55 data<RET>
filt55 data laplace.txt<RET>
********************************************************************
Compiled [Mar 13 15:39:57 2014] Edited [Mar 13 15:39:36 2014]
fix_skew
---------- skewed data correction program Ver.0.17[6.Aug.2010] --------
usage: skewfix input_file_name output_file_name x y z t direction angle
input-file : 4byte float or 2byte short data
output-file : 4byte float or 2byte short data
x, y, z, t : dimension in each axis
direction : x or y
angle : rotation angle in degree
ex) $>>skewfix test.sdt test_out.sdt 64 64 5 100 x 2.5<RET>
-----------------------------------------------------------------------
flt2bit
##############################################
# float to bit converter ver.0 #
##############################################
Usage: flt2bit FILENAME width
width: ~100 for cardiac, ~300 for respiration at 100Hz. 0 for acq(default)
Example:
$> flt2bit acq.flt<RET>
$> flt2bit cardio.flt 50<RET>
$> flt2bit respir.flt 150<RET>
Compiled [Aug 27 11:53:41 2019] Edited [Aug 27 11:53:03 2019]
flt2dbl
---------- Float>Double conversion program Ver.0.0[24.Sep.2014] --------
usage: flt2dbl input_file_name (output_file_name)
input-file : 4 byte FLOAT data
output-file : 8 byte DOUBLE data
-----------------------------------------------------------------------
four2one
---------- Float>Byte conversion program Ver.0.4 ---------------------
usage: four2one input_file_name output_file_name [-,-u]
usage: four2one input_file_name output_file_name min max
input-file : 4 byte FLOAT data
output-file : 1 byte SIGNED/UNSIGNED integer data
[-]: zero free conversion.
[-u]: Unsigned short conversion.
min/max: minimum and maximum values corresponding to 0 and 127
-----------------------------------------------------------------------
Compiled [Sep 6 17:07:12 2015] Edited [Sep 6 16:21:28 2015]
four2two
---------- Float>Short conversion program Ver.0.4 --------
usage: four2two input_file_name output_file_name [-,-u]
input-file : 4 byte FLOAT data
output-file : 2 byte SIGNED/UNSIGNED SHORT data
[-]: zero free conversion.
[-u]: Unsigned short conversion.
----------------------------------------------------------
Compiled [May 26 16:00:13 2015] Edited [May 26 16:00:21 2015]
fplot0
-------- 1D binary data display program 0.0(2012.Feb.3) --------
$>fplot file1.sdt<RET>
$>fplot file1.edt -<RET>
'-' flag is used for COMPLEX data.
Data type needs to be FLOAT.
fplot
-------- 1D binary data display program 0.0(2012.Aug.7) --------
$>fplot file1.sdt<RET>
$>fplot file1.edt -<RET>
'-' flag is used for COMPLEX data.
Data type needs to be FLOAT.
freq
#############################################
# Frequency analyzer ver.0.2 #
#############################################
Usage: freq FILENAME
Usage: freq FILENAME FILENAME2
Usage: freq FILENAME FILENAME2 (step) (width) (1k_flag)
FILENAME : Cardiac or Respiratory data(cardio.peak.bit/respir.peak.bit)
FILENAME2: Acquisition trigger data(acq.peak.bit)
step : acq trigger step for frequency data file output (positive integer)
width: time width of moving avarage for frequency data file output (positive integer, msec, 6000 as default)
1k_flag: 1k
Example:
$> freq acq.peak.bit<RET>
$> freq respir.peak.bit<RET>
$> freq respir.peak.bit acq.peak.bit<RET>
$> freq respir.peak.bit acq.peak.bit 40 3000<RET>
$> freq acq1k.peak.bit 1k<RET>
--------------------------------------------
Compiled [Jun 16 13:47:09 2016] Edited [Jun 16 13:46:46 2016]
getnc
####################################################
# Show the number of coils #
####################################################
Usage: getnc coilstr <RET>]
Compiled [Jul 21 17:16:14 2016] Edited [Feb 22 13:29:09 2016]
getnseg
getnseg ver. 0.1 [23.May.2011]
getnseg petable_file_name<RET>
>getnv epi128alt2k
>getnv epi128alt2k4h
getnv
getnv ver. 0.2 [30.Nov.2010]
getnv petable_file_name<RET>
>getnv epi128alt2k
>getnv epi128alt2k4h
getval
getval v1.01 [11/May/2011]
********************************************************************
Usage: getval x_val table_filename
********************************************************************
glm01
---------- glm (glm calculation) Ver.0.0 ---------------
usage: glm data_file model_file (num_sample)
data_file : data filename (float; num_sample x N)
model_file : model filename (ascii; num_sample x nmodel)
num_sample : this parameter is taken from the model data(number of column) as default
output : beta values(data filename + _b)
* Calculate the Pseudo inverse and apply it for all of the data.
--------------------------------------------------------
Compiled [Feb 23 13:31:31 2015] Edited [Feb 23 13:31:28 2015]
glm0
---------- glm (glm calculation Ver.0.0[27.Nov.2014] --------
usage: glm data_file model_file (nsample)
data_file : data filename (float; nsample x N)
model_file : model filename (ascii; nsample x nmodel)
num_sample : this parameter is taken from the model data(number of column) as default
-----------------------------------------------------------------------
Compiled [Feb 10 17:38:19 2015] Edited[Feb 10 17:38:01 2015]
glmdenoise
----- glmdenoise ver. 0.0.0 [23.May.2017] -----
>>glmdenoise [filename_body] [modelfile] -<RET>
>>glmdenoise run1 run1.mc.1D<RET>
>>glmdenoise run1 run1.mc.1D -<RET>
-: Keep the intermediate files
-----------------------------------------
glm
---------- glm (glm calculation) Ver.0.0 ---------------
usage: glm data_file model_file (num_sample)
data_file : data filename (float; num_sample x N)
model_file : model filename (ascii; num_sample x nmodel)
num_sample : this parameter is taken from the model data(number of column) as default
output : beta values(data filename + _b)
* Calculate the Pseudo inverse and apply it for all of the data.
--------------------------------------------------------
Compiled [Jun 13 12:45:23 2016] Edited [Jun 13 12:42:06 2016]
grappa2
The number of processors is 24
------- Grappa recon -------
>grappa data (R) (kernel0 kernel1)
acs: acs data(ro x pe x slice x coil)
data: data(ro x pe' x slice x coil x nvol) to be reconstructed
R: grappa Acceleration factor(>1)
kernel0: grappa kernel size in ro axis (non-zero even number only)
kernel1: grappa kernel size in pe axis (odd number only)
----------------------------
Compiled [Nov 22 17:51:06 2017] Edited [Nov 22 17:54:48 2017]
grdinfo
############################################################
# Show GRD information ver.0.0 [Jan. 26 2012] #
############################################################
Usage: grdinfo FILENAME<RET>
FILENAME : Gradient shape file name(e.g. ss1.GRD)
gsmooth
---------- gsmooth (smoothing with gaussian kernel) Ver.1.3.5 --------
usage: gsmooth input_fname output_fname (s)
usage: gsmooth input_fname output_fname dim1 dim2 dim3 dim4 kerneltype fwhm1 fwhm2 fwhm3 (s)
input-file/output-file : 4byte float or 2byte short 4D data
's': short integer (default: float)
Same smoothing process to SPM
---------------------------------------------------------------------------------
Compiled [Jun 4 14:34:06 2014] Edited [Jun 4 14:33:58 2014]
hdsplit
#############################################################
# Split file into header and data [ver.0.0] 10.Nov.2014 #
#############################################################
This program split file into header and data.
Usage: hdsplit
block_headersize : block header size(byte)
block_datasize : block data size(byte)
file_headersize : file header size(byte); optional (default value is 0)
File size = file_headersize + (block_headersize + block_datasize) x N
headk
#########################################################
# take head data from the file. #
#########################################################
Usage: headk FILENAME nbyte [-]
[-]: splitting into 2 data files
Output file name is FILENAME_hd
nbyte: byte number for the header part
Example:
$> headk run.nii 348 <RET>
$> headk run.nii 348 - <RET>
(v1.0.3)
Compiled [Mar 13 17:33:17 2017] Edited [Mar 13 17:15:45 2017]
heisei
heisei [year conversion script ver. 0.0 12.Dec.2008]
--------------------------------------------
heisei [heisei_year]<RET>
>heisei 12<RET>
hist
---------- Make-histgram program Ver.0.02-------------------- --------
usage: hist input_file_name output_file_name [hsize] [min] [max]
input-file : 4 byte FLOAT data
output-file : Ascii data
hsize : number of the bins(default:256)
min : minimum for histgram binning(default:minimum data)
max : maximum for histgram binning(default:maximum data)
-----------------------------------------------------------------------
Compiled [Dec 14 18:01:19 2018] Edited [Dec 14 18:01:17 2018]
When NAN values are included, they will be skipped.
>hist_maci a a.txt 10
NAN values were found.(2/11,27.2727%)
Number of data = 9
Minimum data = 1
Maximum data = 105
Number of the bins = 10
Width of the bins = 10.4
Target range : (1 ~ 105)
Done![hist]
homodyne3d
##############################################
# 3D homodyne processing [ver.0.0] #
##############################################
This program does homodyne processing on 3d data(for float complex data)
Usage: homodyne
dim1: data matrix size in the 1st dimension
dim2: data matrix size in the 2nd dimension(oooooo)
dim3: data matrix size in the 3rd dimension(*******)
recon_dim2: reconstracted data's matrix size in the 2nd dimension
recon_dim3: reconstracted data's matrix size in the 3rd dimension
offset_dim2: data offset for the 2nd dimension(0 as default; xxooooooxxx)
offset_dim3: data offset for the 3rd dimension(0 as default; xxxx*******x)
voffset1: voxel offset value ratio(0.5 for half fov1) for dim1
voffset2: voxel offset value ratio(0.5 for half fov2) for dim2
voffset3: voxel offset value ratio(0.5 for half fov3) for dim3
input data : edt file as float(partially acqired k-space data)
output data : sdt file as float(image data processed by homodyne algorithm)
---------------------------------------------
Compiled [Jan 20 15:29:03 2015] Edited [Jan 20 15:15:03 2015]
homodyne
The number of processors is 8
The number of threads is 3
###########################################
# homodyne processing [ver.0.1] #
###########################################
This program does homodyne processing on 2d data(for float data)
Usage: fftcomplex
dim1: data's 1st dimension
dim2: data's 2nd dimension(oooooo)
recon_dim2: reconstracted data's 2nd dimension(xxxoooooo)
input data : edt file as float(partially acqired k-space data)
output data : sdt file as float(image data processed by homodyne algorithm)
---------------------------------------------
Compiled [Sep 3 17:21:28 2014] Edited [Sep 3 16:14:09 2014]
hsv2rgb
#########################################################
# HSV to RGB conversion [ver.0.0] #
#########################################################
This program convert HSV to RGB.
Usage: hsv2rgb h_val s_val v_val (-)<RET>
Usage: hsv2rgb rgb_file.txt (-)<RET>
- : reverse(RGB->HSV)
Compiled [Oct 8 14:32:01 2014] Edited [Oct 8 14:31:58 2014]
human3d_1.35
----- Processing for Human3D(T1T2 or T1) ver. 1.35 [31.Jul.2008] -----
>>human3d [filename_body_t1] [filename_body_t2]<RET>
>>human3d [filename_body_t1]<RET>
This program is available for SAGGITAL images(phi=0 or 90)
ex.) [for 3d-1.t1.fid 3d-1.t2.fid]
$>human3d 3d-1.t1 3d-1.t2
output file: 3d-1.t1t2.sdt/spr 3d-1.t1t2_analyze/3d-1.img/hdr
Use human3d_tr for transversal 3D image.
-----------------------------------------
human3d_140
----- Processing for Human3D(T1T2 or T1) ver. 1.40b [13.May.2009] -----
>>human3d [filename_body_t1] [filename_body_t2] (Threshold) (-N)<RET>
>>human3d [filename_body_t1] (Threshold) (-N)<RET>
This program is available for SAGGITAL images(phi=0 or 90)
Threshold(option): Upper threshold for normalization.
-N: No left-side marker
-F: FLOAT output(without marker)
(You cannot use both of -N and -F)
ex.) [for 3d-1.t1.fid 3d-1.t2.fid]
$>human3d 3d-1.t1 3d-1.t2
$>human3d 3d-1.t1 3d-1.t2 98.5 -N
output file: 3d-1.t1t2.sdt/spr 3d-1.t1t2_analyze/3d-1.img/hdr
Threshold is used for normalization(normal, 97 for default)
Use human3d_tr for transversal 3D image.
-----------------------------------------
human3df
----- Processing for Human3D(T1T2 or T1) ver. 1.36 [16.Sep.2008] -----
>>human3df [filename_body_t1] [filename_body_t2]<RET>
>>human3df [filename_body_t1]<RET>
This program is available for SAGGITAL images(phi=0 or 90)
ex.) [for 3d-1.t1.fid 3d-1.t2.fid]
$>human3d 3d-1.t1 3d-1.t2
output file: 3d-1.t1t2.sdt/spr 3d-1.t1t2_analyze/3d-1.img/hdr
Use human3d_tr for transversal 3D image.
-----------------------------------------
human3dNIFTI_flip
----- Processing for Human3D(T1T2 or T1) ver. 1.40b NIFTI [14.Jul.2009] -----
>>human3dNIFTI [filename_body_t1] [filename_body_t2] (Threshold) (-F)<RET>
>>human3dNIFTI [filename_body_t1] (Threshold) (-F)<RET>
Threshold(option): Upper threshold for normalization.
-F: FLOAT output(without marker)
ex.) [for 3d-1.t1.fid 3d-1.t2.fid]
$>human3dNIFTI 3d-1.t1 3d-1.t2
$>human3dNIFTI 3d-1.t1 3d-1.t2 98.5 -F
output file: 3d-1.t1t2.sdt/spr 3d-1.t1t2_analyze/3d-1.img/hdr
Threshold is used for normalization(normal, 97 for default)
***This version doesn't rotate the 3d volume. For NIFTI. ***
No left side marker on the result.
-----------------------------------------
human3dNIFTI
----- Processing for Human3D(T1T2 or T1) ver. 1.40b NIFTI [14.Jul.2009] -----
>>human3dNIFTI [filename_body_t1] [filename_body_t2] (Threshold) (-F)<RET>
>>human3dNIFTI [filename_body_t1] (Threshold) (-F)<RET>
Threshold(option): Upper threshold for normalization.
-F: FLOAT output(without marker)
ex.) [for 3d-1.t1.fid 3d-1.t2.fid]
$>human3dNIFTI 3d-1.t1 3d-1.t2
$>human3dNIFTI 3d-1.t1 3d-1.t2 98.5 -F
output file: 3d-1.t1t2.sdt/spr 3d-1.t1t2_analyze/3d-1.img/hdr
Threshold is used for normalization(normal, 97 for default)
***This version doesn't rotate the 3d volume. For NIFTI. ***
No left side marker on the result.
-----------------------------------------
human3d
----- Processing for Human3D(T1T2 or T1) ver. 1.40b [13.May.2009] -----
>>human3d [filename_body_t1] [filename_body_t2] (Threshold) (-N)<RET>
>>human3d [filename_body_t1] (Threshold) (-N)<RET>
This program is available for SAGGITAL images(phi=0 or 90)
Threshold(option): Upper threshold for normalization.
-N: No left-side marker
-F: FLOAT output(without marker)
(You cannot use both of -N and -F)
ex.) [for 3d-1.t1.fid 3d-1.t2.fid]
$>human3d 3d-1.t1 3d-1.t2
$>human3d 3d-1.t1 3d-1.t2 98.5 -N
output file: 3d-1.t1t2.sdt/spr 3d-1.t1t2_analyze/3d-1.img/hdr
Threshold is used for normalization(normal, 97 for default)
Use human3d_tr for transversal 3D image.
-----------------------------------------
ima2pro
ima2pro(pro file maker) ver. 0.00b [7.Aug.2017]
ima2pro file.IMA<RET>
ima2pro file.IMA test.pro<RET>
imainfo
...Saved data check script...
./
imap
---------- imap (intensity map) Ver.1.0.1 2011.Dec.28--------
usage: imap [input_fname_body] distance (threshold)<RET>
[input_fname_body].sdt/spr are used as the input.
Output file name: [input_fname_body]_imap.sdt/spr
distance: distance for detecting peak
threshold: threshold value(%) (default: 10%)
---------------------------------------------------------------------------------
int2float
---------- 4byte integer > Float conversion program Ver.0.2 --------
usage: int2float input_file_name output_file_name
input-file : 4 byte INTEGER data
output-file : 4 byte FLOAT data
-----------------------------------------------------------------------
Compiled [Jul 22 13:14:30 2015] Edited [Jul 22 13:14:18 2015]
jpg2sdt _PDF_
jpg2sdt v0.00
********************************************************************
jpg to sdt converter program
>jpg2sdt test.jpg new.sdt<RET>
>jpg2sdt test.jpg new.sdt -<RET>
'-' can be set for the monochrome output(1byte). Otherwise RGB output.
********************************************************************
Compiled [Dec 10 09:57:54 2015] Edited [Dec 10 09:57:31 2015]
kbhit
---------- keycode display program Ver.0.00 [14.Nov.2012] --------
$>>kbhit<RET>
Press 'q' to quit this program.
-----------------------------------------------------------------------
manhtml
Open the command list page with the default web browser.
>manhtml<RET>
>manhtml stlview<RET>
map2sdt
---------- map2sdt (data conversion program) Ver.0.1 [2012.11.16] --------
BV mapfile to sdt/spr
usage: map2sdt [filename]
-----------------------------------------------------------------
Compiled [Jul 24 16:33:31 2017] Edited[Jul 24 16:37:56 2017]
mapthre
---------- mapthre (value thresholding) Ver.0.1b ---------------------
usage: mapthre input_file_name output_file_name [-r] threshold_value [new_value]
input-file : 4byte float data
output-file : 4byte float data
If you set [new value], the thresholded voxel will have the new value.
-r : reverse thresholding. (Lower value will survive.)
-----------------------------------------------------------------------
Compiled [Feb 16 11:21:05 2018] Edited[Feb 16 11:27:55 2018]
maskpng _PDF_
----- USAGE: maskpng (mask png creator) ------------
> maskpng filenamebody width height in_radius out_radius back_R back_G back_B<RET>
e.g.)
>maskpng mask.png 800 500 25 250 51 51 51 <RET>
----------------------------------------------------------
Compiled [Jul 16 11:45:06 2021] Edited [Jul 16 11:45:04 2021]
mcchk
mcchk(mc check) ver. 0.0 [18.Mar.2020]
mcchk<RET>
mcchk 3<RET>
mcchk 2 2 2 3 3 3<RET>
mcchk -2 2 -2 2 -2 2 -3 3 -3 3 -3 3<RET>
mcerr
mcerr v0.00
********************************************************************
Usage: mcerr ascii_file
-------------------------
********************************************************************
Compiled [Mar 18 15:58:15 2020] Edited [Mar 18 15:58:12 2020]
mcube
The number of processors is 12
mcube v0.00
************ Marching cube polygonisation **************************
Usage: mcube filename -i isovalue (-)<RET>
filename: volume data file name
isovalue: target value for the surface detection
-: making output of the edge voxel data(sdt/spr)
EX) If you have
mcube data.sdt -i 12.5 <RET>
********************************************************************
Compiled [Apr 24 16:57:52 2018] Edited [Apr 24 17:06:25 2018]
mghinfo
======== mgh/mgz header dump program 2019.Apr.25 ========
mghinfo<RET> : show this usage
mghinfo test.mgh <RET> : show header information
mrupdate
mrupdate
Update /usr/local/mac_bin folder for MacOSX environment.
You need to have an administrator privilege.
>mrupdate<RET>
...
...
x mac_bin2/trim_old
This procedure will overwrite your /usr/local/mac_bin folder
Do you want to proceed?[Y/n]
Y
Password:
Done!
nan0
---------- NaN buster program Ver.0.1 ---------------------------------
usage: nan0 input_file_name (output_file_name) (newval)<RET>
input-file : 4 byte Float data
output-file : 4 byte Float data
-----------------------------------------------------------------------
Compiled [Feb 16 11:33:03 2018] Edited[Feb 16 11:34:02 2018]
navcor
navcor v0.0
********************************************************************
Usage: navcor Input_file ro_steps pe_steps (necho)
necho: 0,1,2 or 3(default)
data: complex float values in little endian
********************************************************************
Compiled [Jul 18 11:42:18 2017] Edited [Jun 21 17:08:24 2017]
niftihdr_2dax_sdaq
---niftihdr2d_ax [ver.0.0 2006.4.10]---
niftihdr2d_ax [filename]
niftihdr_2dax
---niftihdr2d_ax [ver.0.1 2012.4.6]---
niftihdr2d_ax [filename]
niftihdr_3d_sdaq
---niftihdr_3d[ver.0.0 2006.4.7]---
niftihdr_3d [filename]
niftihdr_3d
---niftihdr_3d[ver.0.1 2012.4.6]---
niftihdr_3d [filename]
nii2img
---nii2img[ver.0.3 2011.4.20]---
nii2img [filename]<RET>
file name can be ###.hdr or ##img or ###.nii
nii3v
---------- nii3v (convert 3/4 vol data into index data) Ver.0.0 ---------------
usage: nii3v nifti_file
data_file : nifti data filename
-------------------------------------------------------
Compiled [Mar 6 10:03:17 2017] Edited[Mar 6 09:45:32 2017]
niibyte
----- niibyte ver. 0.2 [4.Mar.2017] -----
Conversion to 1 byte[0~255] data
>>niibyte [filename_body] (-/+)<RET>
Input data: NIFTI-1 data
'-' flag setting makes NIFTI-1 float data as the result
'+' flag setting skips automatic intensity correction in space
-----------------------------------------
niidbl
-----niidbl (version 0.0) ----
For NIFTI data type conversion
usage: niidbl test.nii<RET>
--------------------------------------------------
Compiled [Mar 13 11:21:09 2017] Edited [Mar 13 11:03:46 2017]
niiflip2
-----niiflip (version 0.0) ----
For NIFTI data type conversion
usage: niiflip test.nii<RET>
--------------------------------------------------
Compiled [Dec 17 17:00:17 2021] Edited [Dec 17 17:00:14 2021]
niiflip
-----niiflip (version 0.0) ----
For NIFTI data type conversion
usage: niiflip test.nii<RET>
--------------------------------------------------
Compiled [Feb 7 11:38:15 2019] Edited [Feb 7 11:38:11 2019]
niiflt
-----niiflt (version 0.0) ----
For NIFTI data type conversion
usage: niitype test.nii<RET>
--------------------------------------------------
Compiled [Mar 13 11:21:35 2017] Edited [Mar 13 11:02:43 2017]
niitype
-----niitype (version 0.0) ----
For NIFTI data
usage: niitype hdr_filename out_filename Dtype_num
--------------------------------------------------
Compiled [Sep 6 10:38:40 2015] Edited [Sep 6 10:38:28 2015]
noisecv _PDF_
---------- Noise covariance matrix maker Ver.0.0 -------------------
usage: noisecv input_file_name output_file_name ncoil (nvol)
input-file : 4 byte FLOAT data
output-file : 4 byte Float data
ncoil : Number of coils (2nd last dimension)
nvol : Matrix size in the last dimension(default value is 1)
-----------------------------------------------------------------------
Compiled [Aug 17 13:39:55 2017] Edited [Aug 17 13:44:17 2017]
normal
---------- Float data Normalization program Ver.0.2 -------------------
usage: normal input_file_name output_file_name [lowcut %] [highcut %]
input-file : 4 byte FLOAT data
output-file : 4 byte Float data
-----------------------------------------------------------------------
Compiled [Sep 7 14:05:07 2015] Edited [Sep 6 14:35:04 2015]
obj2stl
obj2stl v0.0.0 [24/Apr/2016]
********************************************************************
Usage: obj2stl Input_obj_file (Output_stl_file)<RET>
EX) When you have
$>obj2stl test.obj<RET>
$>obj2stl test.obj test_bin.stl<RET>
********************************************************************
one2four
---------- Unsigned char > Float conversion program Ver.0.0 --------
usage: one2four input_file_name output_file_name<RET>
input-file : 1 byte CHAR data
output-file : 4 byte FLOAT data
--------------------------------------------------------------------
Compiled [Dec 17 10:30:03 2013] Edited [Dec 17 10:29:59 2013]
one2two
---------- Unsigned char > Short conversion program Ver.0.0[1.Jul.2010] --------
usage: one2two input_file_name output_file_name<RET>
input-file : 1 byte CHAR data
output-file : 2 byte SHORT data
-----------------------------------------------------------------------
pctl
---------- Percentile calculation program Ver.0.0[14.Aug.2014] --------
usage: normal input_file_name [percentile/step]
input-file : 4 byte FLOAT data
percentile : percentile value [0-100]
step : percentile step value [0-100] (put the value as a negative value)
-----------------------------------------------------------------------
Compiled [Aug 14 18:19:14 2014] Edited [Aug 14 18:19:08 2014]
peak2s
----- Peak version 1.20 [2015.Aug.28] -----
Endian type (CPU) : Little
Application quit normally.
peak2
----- Peak version 1.20 [2015.Aug.28] -----
Endian type (CPU) : Little
Application quit normally.
peak_m32
dyld: Library not loaded: /sw/lib/libXm.3.dylib
Referenced from: /usr4/local/mac_bin2/peak_m32
Reason: image not found
peak
----- Peak version 1.18 [2011.Dec.20] -----
Endian type (CPU) : Little
Application quit normally.
pf2sdt
>>pf2sdt fid_data (-)
fid_data: without .fid
- : skip dedrift
phadj
---------- Phase data adjustment program Ver.0.1 --------
compare the phases between the 2 data sets and asjust the 1st one
usage: phadj input_file_name input_file_name2 (factor) (output-file)
input-file : 4 byte FLOAT data(wrapped)
input-file2 : 4 byte FLOAT data(reference)
factor : comparison factor (file1 ~ factor x file2)
output-file : 4 byte FLOAT data
---------------------------------------------------------
Compiled [Dec 17 18:02:56 2013] Edited [Dec 17 18:02:40 2013]
phfix
---------- Phase data adjustment program Ver.0.01b --------
ph>2PI: ph=ph-2PI
ph<-2PI: ph=ph+2PI
usage: phfix input_file_name (output_file_name)
input-file : 4 byte FLOAT data
output-file : 4 byte FLOAT data
-----------------------------------------------------------
Compiled [Dec 3 10:03:44 2013] Edited [Dec 3 10:03:40 2013]
phpos
---------- Phase data adjustment program Ver.0.00 --------
ph < 0 : ph = ph + PI
usage: phpos input_file_name (output_file_name)
input-file : 4 byte FLOAT data
output-file : 4 byte FLOAT data
-----------------------------------------------------------
Compiled [Dec 3 15:23:32 2013] Edited [Dec 3 15:23:27 2013]
physioauto
----- physioauto ver. 0.00 [11.Jul.2017] -----
Apply physiofix
>physioauto m0007 170711_01.car<RET>
Output file: m0007-pp.sdt/spr
-----------------------------------------
physiofix
The number of processors is 8
---------- physiofix Ver.0.0.1 -------------------------------------------------
usage: physiofix [input_fname_body] bitfile_acq bitfile_car (bitfile_resp)<RET>
[input_fname_body].sdt/spr or .edt/epr are used as the input.
Output file name: [input_fname_body]-pp.sdt/spr
The spr or epr file needs to have slice_time parameters.
---------------------------------------------------------------------------------
Compiled [Aug 15 11:03:53 2017] Edited [Aug 15 11:08:10 2017]
png2sdt
png2sdt v0.00
********************************************************************
png to sdt/sdt to png converter program
>png2sdt test.png new.sdt<RET>
>png2sdt new.sdt new.png<RET>
********************************************************************
Compiled [Dec 9 13:24:50 2015] Edited [Dec 9 13:24:32 2015]
png3d
png3d v0.00
********************************************************************
Two png files to an interlaced 3d png converter program
>png3d test.png test2.png new.png<RET>
********************************************************************
Compiled [Dec 11 08:36:17 2015] Edited [Dec 11 07:58:46 2015]
postproc
CPU type : Little endian
******************************************
postprocv3.8d5b
******************************************
User quit voluntarily.
pp38d4
CPU type : Little endian
******************************************
postprocv3.8d4b
******************************************
User quit voluntarily.
pp38d5
CPU type : Little endian
******************************************
postprocv3.8d5b
******************************************
User quit voluntarily.
pp3d_tst2
The number of processors is 8
The number of threads for fftw is 2
---------- pp3d_tst (postprocessing 3d) Ver.1.3.1 --------
usage: pp3d [input_fname_body] (threshold) (fwhm) (surface shift) (target)<RET>
[input_fname_body].sdt/spr are used as the input.
Output file name: [input_fname_body]_dT.sdt/spr
threshold: threshold value(%) (0% -- default)
fwhm: smoothing kernel's fwhm for the original data (ratio, 1:full size -- default, 0: no-smoothing)
surface shift: surface shift for volume clipping (0-default, positive value for inflate. 999 for no volume clip)
target intensity voxel (%) (highest intensity:100 -- default)
The output file has float type data.
$>pp3d mprage01<RET> is equivalent to $>pp3d mprage01 0 1 999 90<RET>
-----------------------------------------------------------
Compiled [Sep 8 16:23:01 2015] Edited [Sep 7 13:44:03 2015]
pp3d_tst
The number of processors is 8
The number of threads for fftw is 2
---------- pp3d_tst (postprocessing 3d) Ver.1.24 --------
usage: pp3d [input_fname_body] (threshold) (fwhm) (surface shift) (target)<RET>
[input_fname_body].sdt/spr are used as the input.
Output file name: [input_fname_body]_dT.sdt/spr
threshold: threshold value(%) (0% -- default)
fwhm: smoothing kernel's fwhm (ratio, 1:full size -- default, 0: no-smoothing)
surface shift: surface shift for volume clipping (0-default, positive value for inflate. 999 for no volume clip)
target intensity voxel (%) (highest intensity:100 -- default)
The output file has float type data.
$>pp3d mprage01<RET> is equivalent to $>pp3d mprage01 0 1 999 90<RET>
-----------------------------------------------------------
Compiled [May 20 15:01:35 2014] Edited [May 17 09:49:44 2013]
pp3d
The number of processors is 8
The number of threads for fftw is 2
---------- pp3d (postprocessing 3d) Ver.1.1.0c 2012.Nov.29--------
usage: pp3d [input_fname_body] (threshold) (fwhm) (surface shift) (target)<RET>
[input_fname_body].sdt/spr are used as the input.
Output file name: [input_fname_body]_dT.sdt/spr
threshold: threshold value(%) (15% -- default)
fwhm: smoothing kernel's fwhm (ratio, 1:full size -- default, 0: no-smoothing)
surface shift: surface shift for volume clipping (0-default, positive value for inflate. 999 for no volume clip)
target intensity voxel (%) (highest intensity:100 -- default)
The output file has float type data.
$>pp3d mprage01<RET> is equivalent to $>pp3d mprage01 15 1 0 100<RET>
-----------------------------------------------------------------
ppall
----- ppall ver. 0.00 [11.Jul.2017] -----
Apply mcafni glmdenoise despike physiofix ssc2
>ppall [sdt/spr filenamebody] [sdt/spr filenamebody for mcafni] [target volume number] [carfile name] <RET>
e.g.)
>ppall m0007 170711_00.car<RET>
>ppall m0007 ../0006/m0006 0 170711_00.car<RET>
Output file: m0007-aMC_gdnDs-pp.SC.sdt/spr
-----------------------------------------
pp
CPU type : Little endian
******************************************
postprocv3.8d5b
******************************************
USAGE: pp [-flags {args}] inputname outputname
flags: -help
displays help for running postproc
-intype (0 = FID,1 = EDT,2 = SDT)
type of input file, defaults to FID
-outtype (1 = EDT,2 = SDT,3 = IMG)
type of output file, defaults to SDT
-dc
do dc correction
-reg
do registration
-zero
do zero filling
-physiofix
do physiofix(respiratory+cardiac)
-physiofix1
do physiofix(respiratory)
-physiofix2
do physiofix(cardiac)
tablib search path = .:$HOME/vnmrsys/tablib:/usr4/vnmr1/vnmrsys/tablib:/vnmr/tablib
Compiled [Mar 30 13:48:36 2017] Edited [Mar 30 13:28:40 2017]
ptview
----- PT Viewer -----
usage: ptview datafile <RET>
datafile : Ascii data
-----------------------------------------------------------------------
Compiled [Apr 17 15:17:12 2017] Edited [Apr 17 14:54:44 2017]
pure
Making pure tones
1:600Hz2:1200Hz3:1800Hz4:2400Hz5:3000Hz6:3600Hz7:4200Hz8:4800Hz9:5400Hz10:6000Hz11:6600Hz12:7200Hz13:7800Hz14:8400Hz15:9000Hz16:9600Hz17:10200Hz18:10800Hz19:11400Hz20:12000Hz21:12600Hz22:13200Hz23:13800Hz24:14400Hz25:15000Hz26:15600Hz27:16200Hz28:16800Hz29:17400Hz
raxis _PDF_
raxis ver. 0.2c [2.Oct.2013]
raxis [file name body] (x) (y) (s) (v)<RET>
You should have [file name body].sdt/spr or .edt/epr
When you have both of sdt and edt, the sdt is taken.
(x) (y) (s) (v) : new axis
>raxis run1 2 -3 1 4
readpe
#######################################################################
# Read petable(test) [ver.0.00] 28.Jul.2011 #
#######################################################################
Usage: readpe petable_file_name
Usage: readpe petable_file_name<RET>
refcor
refcor v0.0
********************************************************************
Usage: navcor Input_file np nvol<RET>
Input_file : epi data to be corrected
data format should be complex float values in little endian
np : readout steps as float complex
nvol : number of volumes (the 1st one should be the reference data)
********************************************************************
Compiled [Sep 27 16:40:43 2016] Edited [Sep 27 16:42:22 2016]
regrid
#######################################################################
# make complex data on the 1D grid [ver.0.00] 12.Dec.2016 #
#######################################################################
Usage: regred data_file traj_file_name output_file<RET>
input/output data: float binary data
traj_file : trajectory data as ascii
Compiled [Dec 12 17:49:51 2016] Edited [Dec 12 17:45:31 2016]
reo
reo v1.05b [24/Feb/2012]
********************************************************************
Binary data reorder program
Usage: reo Input_datafile order_file data_unit <->
data_unit's unit is Byte.
-: This flag is for reverse application of the order file(it means we can change the result back to the original with this)
EX) If you have
$>reo data.edt order.txt 256<RET>
$>more order.txt
1 4 2 5 3
data:1 2 3 4 5 >> 1 3 5 2 4
data:1 2 3 4 5 >> 1 4 2 5 3 <--Reverse case
********************************************************************
resize3dnii
---------- resize3dnii (trimming/expanding voxels for nifti program Ver.0.0) ---------------
usage: resize3dnii nifti_file x0 x1 y0 y1 z0 z1
data_file : nifti data filename
-------------------------------------------------------
Compiled [Mar 7 17:06:59 2017] Edited[Mar 7 16:50:28 2017]
resize3d
----- resize3d ver. 0.16 [13.Mar.2013] -----
>>resize3d [filename_body] x y z<RET>
>>resize3d [filename_body] size(same for 3 dimension)<RET>
>>resize3d [filename_body]<RET> maximum value is set for x,y,z
-----------------------------------------
rm0
---------- zero data removal program Ver.0.0[13.Nov.2013] --------
usage: rm0 input_file_name (output_file_name)<RET>
input-file : 4 byte Float data
output-file : 4 byte Float data
-----------------------------------------------------------------------
Compiled [Nov 13 09:56:20 2013] Edited [Nov 13 09:56:14 2013]
rmvol
rmvol ver. 1.4b [12.Jul.2010]
rmvol [file name body] (volume number to be removed)<RET>
You should have [file name body].sdt/spr or [file name body].edt/epr
When no number is given, only first volume is taken.
roi2sdt
roi2sdt v0.00
********************************************************************
Usage: roi2sdt roi_file (x y z)<RET>
********************************************************************
Compiled [Mar 6 15:23:56 2018] Edited [Mar 6 15:31:17 2018]
s2us
---------- Signed Short>Unsigned Short conversion program Ver.0.11[8.Jun.2010] --------
usage: s2us input_file_name [-r] <RET>
The file will be overwritten.
-r: inverse transition (Unsigned > Signed)
This program won't scale any but shift 32768.
Us(0~65535) <---> S(-32768~32767)
-----------------------------------------------------------------------
sampler
#########################################################
# sample data from the binary file(Ver0.1) #
#########################################################
Usage: sampler FILENAME sample_flag
Output file name is FILENAME_Spl
Example:
$> sampler run.edt 10100010<RET>
$> sampler run.edt `cat textfile`<RET>
Compiled [Jul 8 11:50:44 2014] Edited [Jul 8 11:50:43 2014]
scanlog
Display the scan log for Agilent MRI data
sdt1to3
------- sdt1to3 -------
sdt1to3 ver. 0.0 [11.Jul.2014]
sdt1to3
You should have [file name body].sdt/spr
flag:0-9
1:BLACK-RED
2:BLACK-GREEN
3:BLACK-BLUE
4:GREEN-YELLOW
5:BLUE-PURPLE
6:RED-YELLOW
7:BLUE-CYAN
8:RED-PURPLE
9:GREEN-CYAN
[A]: +alpha channel
sdt1to4
------- sdt1to4 -------
sdt1to4 ver. 0.01 [24.Jul.2014]
sdt1to4
You should have [file name body].sdt/spr
sdt2div
----- Processing for division image(T1/T2:bias reduction) ver. 1.01 [8.Spe.2015] -----
>>sdt2div [filename_body_t1] [filename_body_t2]<RET>
ex.1) [for 3d.t1.sdt 3d.t2.sdt]
$>sdt2div 3d.t1 3d.t2
output file: 3d.t1t2.sdt/spr
ex.2) [put the left marker for monkey scan]
$>sdt2div 3d.t1 3d.t2 m<RET>
-----------------------------------------
sdt2gif
------- sdt2gif -------
sdt2gif ver. 0.0 [27.Jun.2013]
sdt2gif
You should have [file name body].sdt/spr
(The dataType should be BYTE or UWORD)
movie time: total time for the output movie(10s for the default)
sdt2mov
------- sdt2mov -------
sdt2mov ver. 0.1 [18.Aug.2014]
sdt2mov
You should have [file name body].sdt/spr
(The dataType should be BYTE or RGB or RGBA)
fps: frame per second(10Hz for the default)
sdt2nii
----- sdt2nii ver. 0.00 [17.Nov.2016] -----
>>sdt2nii [filename_body] <RET>
-----------------------------------------
sdt2spm
----- sdt2spm ver. 1.45 [29.Jul.2015] -----
>>sdt2spm [filename_body] <RET>
[filename_body]_analyze directory will have analyze format files.
Put '-' to make 4D analyze data.
>>sdt2spm [filename_body] - <RET>
Put '+' to make nifti data.
>>sdt2spm [filename_body] + <RET>
-----------------------------------------
sdt2to4
------- sdt2to4 -------
sdt2to4 ver. 1.1 [6.Sep.2015]
sdt2to4
You should have [file name body].sdt/spr
sdt2v16
----- sdt2v16 ver. 1.3 [16.Jan.2009] -----
>>sdt2v16 [filename_body] [directry to save your data]<RET>
-----------------------------------------
sdt4to1
------- sdt4to1 -------
sdt4to1 ver. 0.0 [6.Jun.2014]
sdt4to1
You should have [file name body].sdt/spr
-: zero-free conversion
-u: unsigned char conversion
sdt4to2
------- sdt4to2 -------
sdt4to2 ver. 1.2 [13.Jul.2007]
sdt4to2
You should have [file name body].sdt/spr
-: zero-free conversion
-u: unsigned short conversion
sdtcal
----- sdtcal ver. 0.0.2c [3.Jul.2014] -----
>>sdtcal [filename_body] [operator] [filename_body2] (filename_output)<RET>
>>sdtcal [filename_body] [operator] [number]<RET>
>>sdtcal [filename_body] [operator] <RET>
-----------------------------------------
sdtcc
----- sdtcc ver. 0.0.1 [2.Jun.2016] -----
>>sdtcc [filename_body] [protocolfile] (cc_min) (p_max)<RET>
>>sdtcc run1 prt.txt<RET>
>>sdtcc run1 prt.txt 0.7 0.00001<RET>
cc_min: displayRange setting in the spr file
p_min : displayRange setting in the spr file
Number in the protocol file:
@: Neglect the volume
-----------------------------------------
sdtcp
----- sdtcp ver. 0.0.0 [25.Jan.2013] -----
>>sdtcp [filename_body] [filename_body2] <RET>
-----------------------------------------
sdtglm
----- sdtglm ver. 0.0.1 [2.Jun.2016] -----
>>sdtglm [filename_body] [modelfile]<RET>
>>sdtglm run1 glm.txt<RET>
Number in the model file:
@: Neglect the volume
*glm file should include a DC model(all one)
-----------------------------------------
sdtln
----- sdtln ver. 0.0.0 [3.Jun.2014] -----
>>sdtln [filename_body] [filename_body2] <RET>
-----------------------------------------
sdtmv
----- sdtmv ver. 0.0.0 [25.Jan.2013] -----
>>sdtmv [filename_body] [filename_body2] <RET>
-----------------------------------------
sdtstat
----- sdtstat ver. 0.0.2 [19.Feb.2016] -----
Statistics along the volume dimension.
>>sdtstat [filename_body] -flag <RET>
flag: -ave, -sqa, -pw, -max, -min, -var, -sdev ,-snr
-----------------------------------------
sdtt
----- sdtt ver. 0.0.1 [2.Jun.2016] -----
>>sdtt [filename_body] [protocolfile] (tmin tmax pmin pmax)<RET>
>>sdtt run1 prt.txt<RET>
>>sdtt run1 prt.txt 3 8 0 0.0001<RET>
tmin tmax pmin pmax: displayRange setting in spr files
Number in the protocol file:
0: Neglect the volume
1: Control volumes
2: Target volumes
-----------------------------------------
sf2stl
---------- Surface file (Freesurfer) conversion(to STL) program Ver.0.00 ------------------------
ex)
$>>sf2stl lh.inflate <RET>
$>>sf2stl lh.inflate lh.curv <RET>
------------------------------------------------------------------
Compiled [Mar 25 14:18:33 2015] Edited [Mar 25 13:15:43 2015]
shimcalc
---------- shimcalc (shimvalue calculation Ver.0.0[6.Feb.2013] --------
usage: shimcalc fmap smap (sfactor)
fmap : filename of field map measured(float binary)
smap : filename of shim map(float binary)
sfactor: filename of shim factor(text data)
-----------------------------------------------------------------------
showa
showa [year conversion script ver. 0.0 12.Dec.2008]
--------------------------------------------
showa [showa_year]<RET>
>showa 50<RET>
show_hdr
----- show_hdr (version 0.14b)----
This routine can be used for Analyze and Nifti data's header
usage: show_hdr hdr_filename
--------------------------------------------------
Compiled [Sep 29 11:19:11 2014] Edited [Sep 29 11:18:50 2014]
showpp
======== showpp (Show parameters from procpar file) 2010.Jul.20 ========
Usage: showpp fid_file_name
ex) $> showpp run1<RET>
shuffle
shuffle v0.00 [23/Jan/2013]
********************************************************************
Usage: shuffle
datafile: ascii data file
outputfile:
The sequential order is randomized for the data.
********************************************************************
shufln
shufln(Shuffle ascii data line by line) v0.00
********************************************************************
Usage: shufln
datafile: ascii data file
outputfile:
The sequential order is randomized for the data.
********************************************************************
Compiled [Aug 5 11:44:45 2014] Edited [Aug 5 11:44:42 2014]
sint2rgb
skew
----- skew ver. 1.0 [4.Aug.2004] -----
>>skew [filename_body] ['x' or 'y'] [angle] [shift]<RET>
>>angle: degrees
>>shift: pixels
ex.) [for run.sdt/spr]
$>skew run y 10 2
output file: run.Ns.sdt/spr
-----------------------------------------
sliceflip
sliceflip ver. 1.0 [12.Jan.2006]
--------------------------------
sliceflip [file name body]<RET>
You should have [file name body].sdt/spr
Slice order will be reversed
smooth2d
---------- smooth2d (fft+gaussian window smoothing) Ver.1.0.0 2012.Jan.11--------
usage: smooth2d [input_fname_body] (fwhm)<RET>
[input_fname_body].sdt/spr are used as the input.
Output file name: [input_fname_body]_sm2.sdt/spr
fwhm: smoothing kernel's fwhm (ratio, 1:full size)
---------------------------------------------------------------------------------
smooth3d
---------- smooth3d (fft+gaussian window smoothing) Ver.1.0.0 2012.Jan.11--------
usage: smooth3d [input_fname_body] (fwhm)<RET>
[input_fname_body].sdt/spr are used as the input.
Output file name: [input_fname_body]_sm3.sdt/spr
fwhm: smoothing kernel's fwhm (ratio, 1:full size)
---------------------------------------------------------------------------------
sound
--- sound volume setting for OSX ---
>sound -t <RET> : Display this usage
>sound <RET> : Display the current volume setting
>sound 0 <RET> : Mute mode ON
>sound 83 <RET> : Set the current volume as 80(%)
splitcar _PDF_
##############################################
# Car data auto-splitter ver.0.0 #
##############################################
Usage: splitcar FILENAME
Only available for car2/car3 data
Example:
$> splitcar 170321-01.car <RET>
Compiled [Mar 22 14:03:02 2017] Edited [Mar 22 13:43:46 2017]
split_coils
split_coils ver. 0.0 [13.Dec.2012]
split_coils [file name body] (ncoil)<RET>
You should have [file name body].sdt/spr
ncoil: number of channels for array coils
splitsdt
----- splitsdt ver. 0.0.0 [26.Jan.2013] -----
>>splitsdt [filename_body] [volumestep] <RET>
-----------------------------------------
split_vol_hdr
------- split_vol_hdr -------
split_vol_hdr ver. 1.0 [16.Jan.2008]
split_vol_hdr
split_vol
------- split_vol -------
split_vol ver. 1.2 [24.Aug.2009]
split_vol
spm2sdt
----- spm2sdt (version 0.23)----
Convert Analyze/NIFTI1/NIFTI2 to sdt/spr
usage: spm2sdt filename<RET>
filename should be ###.hdr or ###.nii
--------------------------------------------------
Compiled [Mar 14 12:13:23 2016] Edited [Mar 14 12:13:20 2016]
spr2hdr
======== spr2hdr (make hdr file from spr file or spr file from hdr file) 0.02 ========
Usage: spr2hdr spr_file_name hdr_file_name<RET>
ex) $> spr2hdr run1.spr<RET>
ex) $> spr2hdr run1.hdr<RET>
ex) $> spr2hdr run1.spr run1.hdr<RET>
-----------------------------------------------------------------
Compiled [Mar 27 17:03:43 2017] Edited [Mar 27 16:31:12 2017]
srf2stl
---------- SRF > STL file conversion program Ver.0.00 ------------------------
ex) $>>srf2stl test.srf<RET>
------------------------------------------------------------------
Compiled [Apr 21 12:06:03 2016] Edited [Apr 21 12:06:00 2016]
srfinfo
---------- SRF file info program Ver.0.00 ------------------------
ex) $>>srfinfo test.srf<RET>
------------------------------------------------------------------
Compiled [Apr 13 16:49:00 2017] Edited [Mar 25 13:13:39 2015]
ssc2
ssc v2.00
********************************************************************
With sinc + Lanczos_window interporation
Usage: ssc Input_file (without .sdt extension)
spr file must have 'tr' and 'slice_time' parameters appropriatelly.
interpolation flag: 0-linear, n-sinc+Lanczos (default: 5)
EX) If you have
ssc data<RET>
********************************************************************
Compiled [Sep 16 12:12:34 2016] Edited [Sep 16 12:14:40 2016]
ssc
Slice scan time correction program
ssc v1.06
********************************************************************
With sinc + Lanczos_window interporation
Usage: ssc Input_file (without .sdt extension) slice_file
EX) If you have
ssc data slice.txt<RET>
more slice.txt
1 4 2 5 3 6
The 2nd slice was taken at 4th time point.
********************************************************************
Compiled [Jul 25 16:22:38 2014] Edited [Jul 25 16:22:36 2014]
starc_tst
The number of processors is 8
---------- starc program Ver.0.02b --------
usage: starc input_file_name ncoil nov (method) <RET>
input-file : 4byte float data
ncoil : size in the 2nd last dimension(number of coil to be merged)
nov : size in the last dimension(volumes)
method: 0 for Sum of Square, 1 for STARC(default)
ex) $>>starc test.sdt 4 100<RET>
4 coils/100 volumes case
---------------------------------------------
Compiled [Aug 7 11:07:43 2017] Edited [Aug 7 11:12:07 2017]
starc
The number of processors is 24
---------- starc program Ver.0.00 --------
usage: starc input_file_name ncoil nov (method)<RET>
input-file : 4byte float data
ncoil : size in the 2nd last dimension(number of coil to be merged)
nov : size in the last dimension(volumes)
method: 0 for Sum of Square, 1 for STARC(default)
ex) $>>starc test.sdt 4 100<RET>
4 coils/100 volumes case
---------------------------------------------
Compiled [May 2 15:11:43 2017] Edited [May 2 14:46:57 2017]
stat1d
======== stat1d (display stat for 1D data array) 0.00 2012.Feb.29 ========
Usage: stat1d sdt_file_name_body<RET>
ex) $> stat1d spuls<RET>
stlbin
stlbin v0.0.0 [7/Apr/2016]
********************************************************************
Usage: stlbin Input_stl_file <RET>
EX) When you have
$>stlcolor test.stl<RET>
********************************************************************
Convert the ASCII stl file to the binary stl file
stlcat
stlcat v0.0.0 [7/Apr/2016]
********************************************************************
Combine the two binary stl files
Usage: stlcat Input_stl_file1 Input_stl_file2 <RET>
EX) When you have
$>stlcolor test1.stl test2.stl<RET>
********************************************************************
stlcnt
stlcnt v0.0.0 [18/Apr/2016]
********************************************************************
Usage: stlcnt Input_stl_file <RET>
EX) When you have
$>stlcnt test.stl<RET>
********************************************************************
Compiled [Apr 19 13:46:45 2018] Edited [Apr 19 13:54:05 2018]
stlcolor
stlcolor v0.0.0 [7/Apr/2016]
********************************************************************
Usage: stlcolor Input_stl_file (r_val g_val b_bal) <RET>
r_val : red value(0~31)
g_val : green value(0~31)
b_val : blue value(0~31)
EX) When you have
$>stlcolor test.stl 31 10 5<RET>
********************************************************************
stlinfo _PDF_
---------- STL file info program Ver.0.00 ------------------------
ex) $>>stlinfo test.stl<RET>
------------------------------------------------------------------
Compiled [Mar 25 14:19:49 2015] Edited [Mar 14 09:43:56 2015]
stlsm _PDF_
stlsm v0.0.0
********************************************************************
Usage: stlsm Input_stl_file Output_stl_file repeat_num<RET>
EX) When you have
$>stlsm test.stl test_sm.stl<RET>
$>stlsm test.stl test_sm.stl 5<RET>
********************************************************************
Compiled [Jun 7 16:47:19 2019] Edited [Jun 7 16:47:18 2019]
stltrans
---------- STL file transformation program Ver.0.00 ------------------------
stltrans
ex) $>>stltrans test.stl testX.stl 2 2 2<RET>
ex) $>>stltrans test.stl testX.stl 2 2 2 100 0 0<RET>
------------------------------------------------------------------
Compiled [Apr 20 17:06:10 2018] Edited [Apr 20 17:14:49 2018]
stlview _PDF_
----- STL Viewer -----
usage: stlview datafile <RET>
datafile : STL data(BINARY/ASCII STL)
-----------------------------------------------------------------------
Compiled [Nov 16 11:31:20 2016] Edited [Nov 16 11:30:50 2016]
swatch
swatch v0.00
********************************************************************
Stop watch program
Usage: swatch (s) (Output_file)
s:silent flag(no display for every second)
Key control:
.: Display the current time
q: Quit the program
Q/ESC: Quit the program and make an output file
Default outputfile name is swatch_??.txt
********************************************************************
Compiled [Aug 13 16:04:20 2014] Edited [Aug 13 16:04:14 2014]
t2fit
t2 fitting v0.00
********************************************************************
t2fit on sdt/spr files
Usage: t2fit Input_filenamebody
te values need to be set in the spr file and the number of te must be equal to dim4(volume)
result
*_t2.sdt/spr : maps 3 volumes(1-T2Map, 2-PDMap, 3-R^2Map)
*_fit.sdt/spr : theoretical data based on the fit
EX) If you have
t2fit data<RET>
********************************************************************
Compiled [Sep 14 17:48:53 2016] Edited [Sep 14 17:50:49 2016]
temporalfilt
[44;37mtemporalfilt Version:: 0.02_check (Author :: Shubham Gupta 2012.March.23)[0;0m
*************************************************************************************************************
Usage: temporalfilt -data
-acc: Defines the accelaretion for reconstruction for phase encode dimension
Example: ./temporalfilt -data epi04 -recon epi04.filt -acc 2
File format: InputData and OutputData are SDT files. Do *NOT* put the extension (neither .edt nor .epr).
Optional: -remove
Remove means that the 1st volume of the -data is skipped (reference scan).
Optional: -killpix
Number pix defined by killpix will be destroyed at the notch site
Defult value = 3
Optional: -butter
-butter will perform a low pass filtering with a Butterworth filter
Defult = no Butterworth filtering
Optional: -ord
-ord will set Butterworth filter order to n
Defult = 8
Optional: -cutoff
-cutoff will set Butterworth filter cutoff to Wn
Wn should be between 0 and 1
Defult = 0.707
Example: temporalfilt -data epi04.bsi -recon epi04.filt -acc 2 -remove -killpix 2 -butter -ord 8 -cutoff 0.707
*************************************************************************************************************
tgrappa3
The number of processors is 24
------- TGrappa recon -------
>tgrappa data (R) (kernel0 kernel1)
data: acs data(ro x pe x slice x coil)
R: grappa Acceleration factor(>1)
kernel0: grappa kernel size in ro axis (non-zero even number only)
kernel1: grappa kernel size in pe axis (odd number only)
epr file must have tsns parameters(e.g. tsns: 4 3 2 1 for R=4)
----------------------------
Compiled [Nov 27 13:11:55 2017] Edited [Nov 27 11:59:28 2017]
tgrappa
[44;37mtGrappa Version:: 0.02_check (Author :: Shubham Gupta 2012.Feb.6)[0;0m
*************************************************************************************************************
Usage: tGrappa -data
-block: Defines the block size for reconstruction for phase encode dimension
: For tgrappa block size is same as Acceleration Factor
Example: ./tGrappa -data epi04 -recon epi04.recon -block 2 2 1
File format: InputData and OutputData are EDT files. Do *NOT* put the extension (neither .edt nor .epr).
Optional: -remove
Remove means that the 1st volume of the -data is skipped (reference scan).
Optional: -window
Window[0] represent READ POINTS to be read during reconstruction and must be ODD.
Window[1] represent ACS LINES to be read during reconstruction and must be EVEN.
Default values for window is <3><4> .
Increaseing the window size may or may not improve the reconstruction quality but
it will make the reconstruction slow.
Reconstruction quality depends and time depends on number of weights being calculated.
This number is given by (window[1] x window[2] x ncoil).
*************************************************************************************************************
tif2sdt
tif2sdt v0.00
********************************************************************
tiff to sdt converter program
>tif2sdt test.tif new.sdt<RET>
>tif2sdt test.tif<RET>
********************************************************************
Compiled [Jul 14 15:58:38 2016] Edited [Jul 14 15:58:36 2016]
tmpck
DATE A C E F A_temp C_temp E_temp F_temp
170327144741 1340 1057 1367 1084 15.58 68.34 14.61 48.17
170323135906 1332 1056 1361 1084 15.92 69.09 14.79 48.17
170317095001 1316 1056 1346 1085 16.59 69.09 15.33 47.43
170310143528 1318 1054 1348 1084 16.51 70.58 15.24 48.17
170307151654 1338 1056 1368 1083 15.67 69.09 14.58 48.92
170302152356 1178 1014 1208 1056 22.41 99.21 21.15 69.09
170224142422 1239 1054 1264 1082 19.84 70.58 18.79 49.67
170217174044 1316 1054 1336 1083 16.59 70.58 15.75 48.92
170206154522 1264 1054 1294 1083 18.79 70.58 17.52 48.92
170123181455 1253 1054 1276 1084 19.25 70.58 18.28 48.17
trans_coord
The number of processors is 24
---------- 4d binary data transform program Ver.0.19[1.Aug.2012] --------
usage: trans_coord input_file_name output_file_name x y z t trans_x trans_y trans_z trans_t
input-file : any binary data
output-file : same as the input data
x, y, z, t : dimension in each axis
trans_x, trans_y, trans_z, trans_t : swap axis
ex) $>>trans_coord test.sdt test_out.sdt 64 64 5 100 1 3 -2 4<RET>
-------------------------------------------------------------------------
trchk2
tr check program
trchk
tr check program
trigclick
Trigger -> Mouse click conversion program ver.0.04
trigkey
---------- trigger> key up/down event conversion program Ver.0.0 --------
usage: trigbacktick (CGKeyCode) (n) (Modifier CGKeyCode)<RET>
CGKeyCode : 49(space),50(backquote)
n : Number of triggers to be detected
Hit q/Q key to quit the program.
/System/Library/Frameworks/Carbon.framework/Frameworks/HIToolbox.framework/Headers/Events.h
Compiled [Jun 7 11:25:04 2017] Edited [Jun 7 10:44:44 2017]
trigspc
trigger -> spacekey press conversion program
NI-DIO device required.
trimbyte
---------- trim byte program Ver.0.00 -----------
usage: >trimbyte input_file_name start1 end1 start2 end2 ... (endall)<RET>
input-file : Any binary data
output-file : Binary data
ex) $>>trimbyte test.sdt 5 10 30 39<RET> 5~10, 30~39 will be taken among 0~39.
$>>trimbyte test.sdt 0 10 30 40 90 <RET> 0~10, 30~40 will be taken among 0~90.
--------------------------------------------
Compiled [Feb 6 17:19:33 2017] Edited [Feb 6 17:07:11 2017]
trim
---------- trim program Ver.0.12 -----------
usage: >trim input_file_name output_file_name x y s t xStart xEnd yStart yEnd sStart sEnd tStart tEnd <RET>
>trim input_file_name output_file_name x y xStart xEnd yStart yEnd <RET>
input-file : Any binary data
output-file : Binary data: Outside of the original data will be filled with NULL(zero) data
x, y, s, t : dimension in each axis
xStart xEnd
yStart yEnd
sStart sEnd
tStart tEnd
ex) $>>trim test.sdt test_out.sdt 64 64 5 100 0 63 0 63 0 4 10 20<RET>
$>>trim test.sdt test_out.sdt 100 10 20<RET> This is equivalent.
Taking 10-20 volumes
--------------------------------------------
Compiled [Jul 11 13:16:05 2016] Edited [Jul 11 13:16:02 2016]
trktrans
---------- TRK transformation program Ver.0.00 ------------------------
$>>trktrans
e.g.
$>>trktrans test.trk test_trans.trk 1 1.2 1.2 100 100 100<RET>
------------------------------------------------------------------
Compiled [Mar 2 18:33:33 2017] Edited [Mar 2 18:33:21 2017]
trkview _PDF_
----- TRK Viewer -----
usage: trkview datafile <RET>
datafile : TRK BINARY data
-----------------------------------------------------------------------
Compiled [Apr 6 15:21:34 2016] Edited [Apr 6 15:21:33 2016]
trm2qtn
---------- Make Quarternion from Rotation Matrix Ver.0.02[11.Mar.2010] --------
TR =
x1 x2 x3 x4
y1 y2 y3 y4
z1 z2 z3 z4
0 0 0 1
-----------------------------
Case 1 [4x4 transformation matrix >> Quaternion conversion]
usage: trm2qtn x1 x2 x3 x4 y1 y2 y3 y4 z1 z2 z3 z4<RET>
Output: qb,qc,qd,qx,qy,qz,dx,dy,dz,qfac
ex) $>>trm2qtn 1 0 0 0 0 1 0 0 0 0 1 0<RET>
-----------------------------
Case 2 [Quaternion >> 4x4 transformation matrix conversion]
Output: x1 x2 x3 x4 y1 y2 y3 y4 z1 z2 z3 z4
usage: trm2qtn qb qc qd qx qy qz dx dy dz qfac<RET>
ex) $>>trm2qtn 0.7 0.7 0 -90 -90 100 1 1 10 1<RET>
-----------------------------
Case 3 [ make inverse matrix of 4x4 transformation matrix ]
Output: x1 x2 x3 x4 y1 y2 y3 y4 z1 z2 z3 z4
usage: trm2qtn x1 x2 x3 x4 y1 y2 y3 y4 z1 z2 z3 z4<RET>
ex) $>>trm2qtn 1 0 0 0 0 1 0 0 0 0 1 0<RET>
-----------------------------------------------------------------------
tsense
tSense v0.06c-checking [Mauro..Modified by Ken, 2013.Sep.24]
********************************************************************
Usage: tsense -full
Optional: -noise
-accf: 1st variable is the acceleration factor. following r variables are the order in which each shot must be put.
-remove means that the 1st volume of the SENSE data is skipped (reference scan).
-ref specifys the volume to be used for calculating sensitivity map(default:0 for the nearest volume, n for the nth volume, -1 for the average of the all volumes)
Example:
> ./tsense_maci -full testrun.pp -remove -recon testrecon -accf 2 2 1 -mask test.msk
---File format---
sensedata, noisedata and fulldata are EDT files. Do *NOT* put the extension (neither .edt nor .epr).
maskdata: assumed to be .sdt single-volume, of appropriate data-size, possibly generated with Mausk program.
********************************************************************
tsns_pp2
------- tsns_pp2 -------
tsns_pp2 ver. 0.03 [7.Jul.2015]
tsns_pp2
You should have [file name body].sdt/spr
nsample : number of sample to calculate the correction value(nsample x R <= nov, the defalt value is 60)
R parameter is needed to be set properly in .spr file
tsns_pp
------- tsns_pp -------
tsns_pp ver. 2 [4.Oct.2011]
tsns_pp
You should have [file name body].sdt/spr
R parameter is needed to be set properly in .spr file
-: summation method(default: multiplication method)
ttest
--------------- ttest (ttest for binary files) Ver.0.02d -------------
usage: ttest datafile desigefile_B resultfile [resultfile2]
datafile : 4byte float data
resultfile : t-value 4byte float data
resultfile2: p-value 4byte float data
ex) ttest run1.sdt prt.txt Result
Number in the protocol file:
0 or @: Neglect the volume
1: Control volumes
2: Target volumes
Pvalues are for both-tailed text(p2). One-tailed t-test's pvalues can be defined as p1=(1+p2)/2
-----------------------------------------------------------------------
Compiled [Jun 13 12:38:05 2016] Edited [Jun 13 12:37:52 2016]
two2four
---------- Short > Float conversion program Ver.0.2 ----------------
usage: four2two input_file_name output_file_name [-]
input-file : 2 byte SIGNED/UNSIGNED SHORT data
output-file : 4 byte FLOAT data
[-]: Conversion from Unsigned short.
---------------------------------------------------------------------
Compiled [May 26 16:00:23 2015] Edited [May 26 16:00:01 2015]
two2one
---------- Short > Unsigned char conversion program Ver.0.0[30.Jun.2004] --------
usage: two2one input_file_name output_file_name (upper_threshold)
input-file : 2 byte SIGNED SHORT data
output-file : 1 byte CHAR data
upper_threshold: for trimming DC peak
-----------------------------------------------------------------------
txt2car2
####################################################
# Convert .txt data to .car(Ver.2) #
####################################################
Usage: txt2car2 FILENAME
Output file name is FILENAME + .car/.ext
Example:
$> txt2car2 030512.txt<RET>
by Ken(4. Jul. 2013) v1.0.2
txt2car
#########################################################
# Convert .txt data to .car/.ext #
#########################################################
Usage: txt2car FILENAME
Output file name is FILENAME + .car/.ext
Example:
$> car2txt 030512.txt<RET>
by Ken(11. Dec. 2009) v1.0.2
v16flip
---------- v16 flip (v16 file conversion program) Ver.0.0 [2008.Sep.2] --------
usage: v16flip inputfile_name
input-file : v16 file
------------------------------------------------------------------------------
v16tovmr
v16tovmr v0.0.0 [19/Apr/2012]
********************************************************************
Usage: v16tovmr Input_file (lowcut) (highcut) <RET>
lowcut : low cut value(%) --default=10
highcut : high cut value(%) --default=90
EX) When you have
v16tovmr data<RET>
********************************************************************
vcube
The number of processors is 12
vcube v0.00
************ cube block polygonisation **************************
Usage: vcube filename -i isovalue (-)<RET>
filename: volume data file name
isovalue: target value for the surface detection
-: making output of the edge voxel data(sdt/spr)
EX) If you have
vcube data.sdt -i 12.5 <RET>
********************************************************************
Compiled [Jan 25 13:40:12 2019] Edited [Jan 25 13:40:08 2019]
view2d
###################################################
# MRI data viewer program (2D) [ver.0.21] #
###################################################
Usage: view2d
Supported files:
sdt/spr(float,short)
edt/epr(float,short)
img/hdr(float,short, unsigned short, int, unsigned int, unsigned char)
nii/nii.gz(float,short, unsigned short, int, unsigned int, unsigned char)
fid(float,short)
fdf(float)
dcm/IMA(unsigned int,unsigned short)
amr
vmr
v16
fmr(float,short)
BRIK/HEAD(float,int,short)
mgh(float,int,short,unsigned char)
mgz(float,int,short,unsigned char)
2dseq(float,int,unsigned int,short,unsigned short,char,unsigned char)
Compiled [Mar 31 15:10:47 2017] Edited [Mar 8 14:20:46 2017]
view3d
The number of processors is 24
#################################################
# MRI data viewer program (3D) [ver.0.29] #
#################################################
Usage: view3d
Supported files:
sdt/spr(float,short)
edt/epr(float,short)
img/hdr(float,short, unsigned short, int, unsigned int, unsigned char)
nii/nii.gz(float,short, unsigned short, int, unsigned int, unsigned char)
fid(float,short)
fdf(float)
dcm(unsigned int,unsigned short)
amr
vmr
v16
fmr(float,short)
BRIK/HEAD(float,int,short)
mgh(float,int,short,unsigned char)
mgz(float,int,short,unsigned char)
2dseq(float,int,unsigned int,short,unsigned short,char,unsigned char)
Compiled [Apr 12 15:13:58 2017] Edited [Apr 12 14:51:51 2017]
vmarknii
-----vmarknii (version 0.0) ----
Put a spatial marker for NIFTI data(include float type conversion)
usage: vmarknii [input_nifti_fname] index<RET>
[input_nifti_fname]: NIFTI-1 (only .nii is available)
Output file name: [input_fname_body]_MK3.nii
index: marker index
1 :Min-dim[1]
2 :Max-dim[1]
3 :Min-dim[2]
4 :Max-dim[2]
5 :Min-dim[3]
6 :Max-dim[3]
0 :Remove the markers
--------------------------------------------------
Compiled [Apr 14 09:50:00 2017] Edited [Apr 14 09:27:51 2017]
vmark
---------- vmark (adding volume marker for the data) Ver.1.0.1 2012.Jan.19--------
usage: vmark [input_fname_body] index<RET>
[input_fname_body].sdt/spr are used as the input.
Output file name: [input_fname_body]_MK3.sdt/spr
index: marker index
1 :Min-dim[1]
2 :Max-dim[1]
3 :Min-dim[2]
4 :Max-dim[2]
5 :Min-dim[3]
6 :Max-dim[3]
Minus values : remove the marker
----------------------------------------------------------------------------------
vmr_counter
---------- vmr_counter (voxel counting program) Ver.1.2b Jul.24.2012 --------
usage: vmr_counter inputfile_name (bin size) <RET>
input-file : VMR file
bin size : bin size for the output
--------------------------------------------------------------------------------
voxave
The number of processors is 12
---------- voxave (voxel averaging program) Ver.0.00 --------
usage: voxave file_name_body1 (x,y,z)
input-file1 : [file_name_body].sdt/spr
output-file : [file_name_body]_AVG.sdt/spr
-------------------------------------------------
Compiled [May 28 14:44:36 2019] Edited [May 28 14:44:34 2019]
vstim0
---------- Vstim program Ver.0.12 --------
usage: vstim sequence_filename (ntrig) <RET>
usage: vstim sequence_filename -t (ntrig) <RET>
-t : Test mode with a small window
ntrig : Maximum number of input triggers
*** Keyboard control ***
0-4 : Go back to the initial display(index1-5)
q/Q : Quit the program
----------------------------------------------------------
Compiled [Mar 13 10:39:22 2017] Edited [Mar 13 10:22:01 2017]
vstim
---------- Vstim program Ver.0.12 --------
usage: vstim sequence_filename (ntrig) <RET>
usage: vstim sequence_filename -t (ntrig) <RET>
-t : Test mode with a small window
ntrig : Maximum number of input triggers
*** Keyboard control ***
0-4 : Go back to the initial display(index1-5)
q/Q : Quit the program
----------------------------------------------------------
Compiled [Mar 13 10:39:22 2017] Edited [Mar 13 10:22:01 2017]
wav2sdt
---------- wav2sdt (wav to sdt/spr convertion) Ver.0.00 --------------
usage: wav2sdt input-file
input-file :
output-file :
-----------------------------------------------------------------------
Compiled [Feb 21 09:55:50 2017] Edited [Feb 21 09:41:21 2017]
wavh
############################################################
# header information dump program [ver.0.2] #
############################################################
Usage: fidtst
Usage: fidtst
- : For creating the wave header file
-f : For creating the wave header file + data file
Compiled [Jul 1 10:28:41 2014] Edited [Jul 1 10:28:36 2014]
wnoise
---------- Create white noise as float data Ver.0.0 --------
usage: wnoise output_file_name num_data (ave) (amp)
output-file : 4 byte FLOAT data
ave : average(default:0)
amp : amplitude(default:1)
'srand()' and 'rand()' funtions are used.
rand()'s RANGE: 0 - 2147483647
Output data = amp x (rand()/RAND_MAX - 0.5) + ave
--------------------------------------------------------------------
Compiled [Jan 26 11:19:04 2015] Edited [Jan 26 11:19:02 2015]