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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
filemkmask.maskAlg

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

fileadd_mask.maskAlg
filedel_mask.maskAlg
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spr(epr) file format†

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Basic paramters:†

numDimThe number of dimensions for the data.
dimThe number of data points in each dimension.
dataTypeThe data type. There are five data types supported as given with their corresponding sizes in Table


Attribute ValuesSizeBytes
BYTEsizeof(char)1
WORDsizeof(short)2
LWORDsizeof(ing)4
REALsizeof(float)4
COMPLEX2*sizeof(float)8
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Optional parameters:†

originPosition 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
fovField 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
intervalThe 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
sdtOrientOrientation of data(ax,cor,sag,NULL,xyz,xzy,yxz,yzx,zxy,zyx)
displayRangeTwo 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.
Real2WordScaleScale factor for REAL(float) to WORD(short) conversion
zPosn???
fidNamefid file name as the data source
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RIKEN original parameters†

endianEndian type of the sdt data
ncoilNumber of the receiver coils
RAcceleration factor
petablepetable file name
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Only for epr†

intlvshot interleaving(y or n)
iltsshot combination for group-of-shot interleaving
sssteady state volume scan number(dummy volumes)
RotateThe data needs to be rotated or not(y or n)
tsnsshot order for t-sense
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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: 
    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