Hi FSL group,
I'm interested in obtaining ROI volumes from different regions in the Harvard-Oxford Atlas from my T1 data. I'm looking through the archives for how to do this but I'm getting confused. I would like to verify that my steps are correct:
1. Transform the MNI ROIs into T1 space
a. first get a transformation from T1 to MNI space: flirt -in T1_reorient_brain -ref MNI152_T1_2mm_brain -out T1_to_MNI -omat T1_to_MNI.mat
b. now I need to get MNI_to_T1.mat: convert_xfm -omat MNI_to_T1.mat -inverse T1_to_MNI.mat
c. transform the MNI ROI into T1 space: flirt -in ROI.nii.gz -ref T1_reorient_brain -out ROI_T1.nii.gz -applyxfm -init T1/MNI_to_T1.mat -interp nearestneighbour
2. Get the mean of the ROI: fslmeants -i T1_reorient_brain -m ROI_T1.nii.gz
3. Get the volume of the ROI: fslstats ROI_T1.nii.gz -V | awk '{print $2}'
4. Multiply the result of 2) and 3) to get the ROI volume
5. Account for head size: run sienax and get the vscaling value. Then multiply the result of 4) with the vscaling value.
Any help would be greatly appreciated!
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