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

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 Caution
>
> 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 <mailto:ddcc2442@gmail.com>_
> 443-254-6298
>
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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