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Hello,
I am trying to extract stats from the hippocampal subfield volumes that I have warped to diffusion space.
mri_vol2vol --mov /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lowb.nii.gz --targ /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz --inv --interp nearest --o /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz --reg /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./register.dat --no-save-reg
Then I run
mri_segstats --seg /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --id 550 --id 552 --id 556 --id 557 --id 558 --i /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./fa-masked.nii.gz --sum ${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.fa.stats
using the --i id# from FreeSurferColorLUT.txt.
However, looking at the values of the hippocampal subfield volume I see that the Id's are all in the 200's?
Is there a txt file that has the labelings like in FreeSurferColorLUT.txt for these hippocampal subfields?
Thank you for any help you can provide! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298