Try using mri_binarize with the hipsubfields as input and using --match 231 232
This will create a mask of all voxels that match the numbers

On 4/8/2019 8:49 PM, Daniel Callow wrote:

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Hello,

I am trying to create ROI volumes from the hippocampal subfields I get from

mri_vol2vol --mov /Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}/lowb.nii.gz --targ /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz --inv --interp nearest --o /Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}/lhipp2diff.nii.gz --reg /Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}/register.dat --no-save-reg

 so that I can merge specific hippocampal subfields I want together into a single ROI (like --id 231 and --id 232). However, when looking through the freesurfer options like mri_vol2vol there isn't an option to index to specific segments of the lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz volume I have converted into dti space. 

My plan is to combine the head and body segments and extract average diffusion information from the combined mask.

Anything that can help get me in the right direction would be greatly appreciated!

Daniel Callow

PhD Student, Neuroscience and Cognitive Science

Exercise for Brain Health Lab

University of Maryland, College Park

ddcc2442@gmail.com

443-254-6298

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