External Email - Use Caution
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
*ddcc2...@gmail.com <ddcc2...@gmail.com>*
443-254-6298
On Wed, Mar 6, 2019 at 12:56 PM Greve, Douglas N.,Ph.D. <
dgr...@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
> > _ddcc2...@gmail.com <mailto:ddcc2...@gmail.com>_
> > 443-254-6298
> >
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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