STIMULATE

Last-modified: 2020-02-25 (Tue) 01:54:07 (1524d)

Mask making
spr(epr) file format
sdt file
Commands

Mask making †

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

mkmask.maskAlg

Delete or Add mask manually
1. Draw ROI on the images
2. "Genarete mask"

add_mask.maskAlg

del_mask.maskAlg

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spr(epr) file format †

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Basic paramters: †

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
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	+10^-38～ +10³⁸
LREAL	sizeof(double)	8	+10^-308～ +10³⁰⁸
COMPLEX	2*sizeof(float)	8
ASCII*

'ASCII' and 'UWORD' are supported by view2d/3d.

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Optional parameters: †

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

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RIKEN original parameters †

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)

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Only for epr †

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

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Examples †

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

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sdt file †

binary or ascii data

dim4_loop(dim3_loop(dim2_loop(dim1_loop (data1, data2,...dataN),...),...),...)

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Commands †

 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