History of STIMULATE (No. 13)
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- 1 (2006-11-08 (Wed) 20:02:04)
- 2 (2006-11-08 (Wed) 20:15:22)
- 3 (2007-02-14 (Wed) 00:09:23)
- 4 (2011-06-02 (Thu) 17:02:12)
- 5 (2011-09-08 (Thu) 17:07:26)
- 6 (2012-02-28 (Tue) 22:54:33)
- 7 (2013-06-13 (Thu) 20:17:29)
- 8 (2013-06-27 (Thu) 16:40:31)
- 9 (2013-12-18 (Wed) 20:55:08)
- 10 (2014-03-03 (Mon) 20:51:24)
- 11 (2014-08-10 (Sun) 23:19:32)
- 12 (2015-07-28 (Tue) 10:49:23)
- 13 (2016-07-06 (Wed) 02:39:30)
- 14 (2018-04-03 (Tue) 21:03:42)
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.maskAlgDelete or Add mask manually
1. Draw ROI on the images
2. "Genarete mask"
spr(epr) file format†
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 | +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:†
| 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 |
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) |
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 |
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
sdt file†
binary or ascii data
dim4_loop(dim3_loop(dim2_loop(dim1_loop (data1, data2,...dataN),...),...),...)
Commands†
jpg2sdt png2sdt view2d view3d sdtcp sdtln sdtmv splitsdt sdtt sdtcc sdtglm resize3d_tst sdt2spm sdt2mov spm2sdt sdt2gif sdt1to4 sdt1to3 sdt2to4 sdt4to1 sdt4to2 sdtcal dcm2sdt dcms2sdt eflipsdt wav2sdt sdtstat fid2sdt fdf2sdt pf2sdt map2sdt raxis