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Never mind. I see that I can use those to id #'s to call from FreeSurferColorLUT.txt.
I assume that those Id's are consistent for both left and right hippocampus.
Thanks for the help! *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
On Wed, Mar 6, 2019 at 1:09 PM Daniel Callow ddcc2442@gmail.com wrote:
Hi Doug,
Thank you for your reply!
Unfortunately when I run the same code as before but by calling to /Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt instead of /Applications/freesurfer/FreeSurferColorLUT.txt and using the assosciated --id #'s as shown below
mri_segstats --seg /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz --mul 1000 --ctab /Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt --id 226 --id 205 --id 206 --id 208 --id 209 --id 210 --i /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./radialdiff-masked.nii.gz --sum ${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.radialdiff.stats
I get the following error.
Loading /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest./rhipp2diff.nii.gz
CTABreadASCII(/Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt): badly formed file
No such file or directory
ERROR: reading /Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt
any idea how I could make it a formed file that is compatible?
Best, *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
On Wed, Mar 6, 2019 at 12:56 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
look in $FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt The first number should be the one you are looking for.
On 3/6/19 12:26 PM, Daniel Callow wrote:
External Email - Use CautionHello,
I am trying to extract stats from the hippocampal subfield volumes that I have warped to diffusion space.
mri_vol2vol --mov /Volumes/DANIEL/dti_freesurf/dtrecon/${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 mailto:ddcc2442@gmail.com_ 443-254-6298
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