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:
External Email - Use Caution
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
ddcc2...@gmail.com<mailto:ddcc2...@gmail.com>
443-254-6298
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