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 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 1:09 PM Daniel Callow <ddcc2...@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
> *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 mailing list
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>>
>>
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