Segmenting DTI images

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1

Hi,

I am trying to segment and mask rois on AD/FA/MD/RD images using fsl.I am getting an error about inconsistent mask and image size. this is the command i am using:
fslstats DTI_image_FA -k “$JHUPATH/roi_1_2mm” -m
previously i have used flirt -in $JHUPATH/roi_1 -ref $JHUPATH/roi_1 -applyisoxfm 2 -nosearch -out $JHUPATH/roi_1_2mm -interp nearestneighbour
to change the roi size but with these dimensions i am not sure how to go about this. any advice is helpful! thanks

My info for the dti images is as follows:
data_type FLOAT32
dim1 128
dim2 128
dim3 59
dim4 1
datatype 16
pixdim1 2.734375
pixdim2 2.734375
pixdim3 2.700000
pixdim4 9.000000
cal_max 0.003654
cal_min 0.000000
file_type NIFTI-1+

and for the ROI:
data_type FLOAT32
dim1 91
dim2 109
dim3 91
dim4 1
datatype 16
pixdim1 2.000000
pixdim2 2.000000
pixdim3 2.000000
pixdim4 1.000000
cal_max 0.000000
cal_min 0.000000
file_type NIFTI-1+

2

Hi @ET_123456,

You might find the mrgrid function useful, espcially the -regrid option where you can specify a reference image to resample to.

For future posts, please format any code and terminal outputs by pressing the </> button in the text editor or surrounding the text in tick marks (``) so it looks like this (one tick mark)

or like this (3 tick marks)

Keep in mind you want to regrid the mask with nearest neighbor interpolation, do not touch the scalar maps.

Best,
Steven