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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
*ddcc2...@gmail.com <ddcc2...@gmail.com>*
443-254-6298
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