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 *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 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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Hi Daniel

left and right hippocampus have different indices (17 and 53)

cheers Bruce On Wed, 6 Mar 2019, Daniel Callow wrote:

External Email - Use Caution

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 CallowPhD 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 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 CallowPhD 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
  >
  > _______________________________________________
  > Freesurfer mailing list
  > Freesurfer@nmr.mgh.harvard.edu
  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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