[[FrontPage]]
#contents
[[Manual>>http://www.fmri.brain.riken.jp/~mri/document/stimUsersGuide]]
*Mask making [#f2ba2fa5]
Making mask by using "Stimulate"~
After motion correction,~
1. Average volumes[ave_vol]~
2. Load averaged data(with some smoothing)~
3. Draw ROI on the images~
4. "Generate mask"~
thresholding,connected voxel counting
Adjust the parameters
#ref(mkmask.maskAlg)
Delete or Add mask manually~
1. Draw ROI on the images~
2. "Genarete mask"~
#ref(add_mask.maskAlg)
#ref(del_mask.maskAlg)
*spr(epr) file format [#v59b9449]
**Basic paramters: [#j6101c57]
,numDim,The number of dimensions for the data(=4 for the default).
,dim,The number of data points in each dimension.
,dataType,The data type. There are five data types supported as given with their corresponding sizes in Table (=REAL for the default)
~
|Attribute Values|Size|Bytes|Data Range|h
|BYTE|sizeof(unsigned char)|1|0~255|
|WORD|sizeof(short)|2|-32768 ～ +32767|
|UWORD*|sizeof(unsigned short)|2|0 ～ 65535|
|LWORD|sizeof(int)|4|-2147483648 ～ +2147483647|
|REAL|sizeof(float)|4|+10SUP{-38}～ +10SUP{38}|
|LREAL|sizeof(double)|8|+10SUP{-308}～ +10SUP{308}|
|COMPLEX|2*sizeof(float)|8||
|ASCII*||||
'ASCII' and 'UWORD' are supported by view2d/3d.~
**Optional parameters: [#wac50b7a]
|origin|Position of the center of the first voxel. One value for each dimension. If the origin is not specified, but the fov is, then the image is assumed to be centered: origin = - fov / 2.0 + interval / 2.0|
|fov|Field of view: The distance between the outside edges of the first and last voxel along each dimension; one value for each dimension. If the fov is not specified it is calculated according to: fov = interval * dim|
|interval|The center to center distance between adjacent voxels along each dimension; one value for each dimension. If the interval is not specified it is calculated according to: interval = fov / dim|
|sdtOrient|Orientation of data(ax,cor,sag,NULL,xyz,xzy,yxz,yzx,zxy,zyx)|
|displayRange|Two values giving the low_value and high_value. Voxel values below the low_value will be displayed as black and voxels with values above the high_value will be displayed as white. Voxels with values within the display range are displayed with a grey value that is scaled linearly between the low_value and high_value. |
|Real2WordScale|Scale factor for REAL(float) to WORD(short) conversion|
|zPosn|???|
|fidName|fid file name as the data source|
|sdtName|corresponding sdt file name for the spr file|
**RIKEN original parameters [#w1b35c19]
|endian|Endian type of the sdt data|
|ncoil|Number of the receiver coils|
|R|Acceleration factor|
|petable|petable file name|
|view|view2d parameters(nrow,ncolumn,slice offset,volume offset)|
***Only for epr [#pdf5c3c8]
|intlv|shot interleaving(y or n)|
|ilts|shot combination for group-of-shot interleaving|
|ss|steady state volume scan number(dummy volumes)|
|Rotate|The data needs to be rotated or not(y or n)|
|tsns|shot order for t-sense|
|slice_order|slice order indexes which start from zero|
**Examples [#qbcf2e82]
-A typical stimulate ``.spr'' example:
numDim: 4
dim: 128 128 20 150
origin: -10.000000 -10.000000 0.000000 0.000000
fov: 20.000000 20.000000 2.000000 15.000000
interval: 0.156250 0.156250 1.000000 1.000000
dataType: REAL
displayRange: 0.000000 347.904358
fidName: stimFid.sdt
sdtOrient: sag
-A minimal ``.spr'' example:
dim: 64 64 27 110
-A small ``.spr'' example:
numDim: 4
dim: 64 64 27 110
dataType: REAL
-A ``.epr'' example:
numDim: 4
dim: 64 64 40 628
origin: -9.4500008 -9.4500008 -12.73260 0.000000
extent: 9.4500008 9.4500008 -1.032596 627.0000
fov: 19.20000 19.20000 12.00001 628.0000
interval: 0.3000000 0.3000000 0.3000002 1.000000
dataType: REAL
fidName:run1.fid
sdtOrient:NULL
intlv:y
ilts: 1
Rotate:y
endian:ieee-be
ncoil: 4
R: 1
ss: 3
tsns: 2 1
-A ``ASCII data'' example:
>%more asc5.spr
numDim: 4
dim: 5 5 5 1
dataType: ASCII
>% more asc5.sdt
#Sample ASCII sdt file
#---Slice 1---
1 2 3 4 5
6 7 8 9 10
11 12 13 14 15
16 17 18 19 20
21 22 23 24 25
#---Slice 2---
0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
#---Slice 3---
13 13 13 13 13
13 13 13 13 13
13 13 13 13 13
13 13 13 13 13
13 13 13 13 13
#---Slice 4---
25 25 25 25 25
25 25 25 25 25
25 25 25 25 25
25 25 25 25 25
25 25 25 25 25
#---Slice 5---
25 0 25 0 25
0 25 0 25 0
25 0 25 0 25
0 25 0 25 0
25 0 25 0 25
#EOF
* sdt file [#zc7300d1]
binary or ascii data
dim4_loop(dim3_loop(dim2_loop(dim1_loop (data1, data2,...dataN),...),...),...)
* Commands [#la4bb944]
jpg2sdt
png2sdt
tif2sdt
view2d
view3d
sdtcp
sdtln
sdtmv
splitsdt
sdtt
sdtcc
sdtglm
resize3d
sdt2spm
sdt2mov
spm2sdt
sdt2gif
sdt1to4
sdt1to3
sdt2to4
sdt4to1
sdt4to2
sdtcal
dcm2sdt
dcms2sdt
eflipsdt
wav2sdt
sdtstat
fid2sdt
fdf2sdt
pf2sdt
map2sdt
raxis