Here’s the script that I’m running and the merged stderr stdout.  I’ve also 
tried various permutations of mris_sample_parc using the -t flag and using 
different LUTs than the one I made.  Also copying the log here incase the text 
files get removed.

Thanks,
jared


./targetAnnotStats.sh: line 21:  4934 Segmentation fault      (core dumped) 
mris_anatomical_stats -a ${SUBJECTS_DIR}/${sub}/label/lh.${targ}_annot.annot -b 
${sub} lh >> log.txt 2>&1
reading parcellation volume from 
/data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/s111_bla_8mm_orig2.nii.gz...
reading input surface 
/data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white...
could not open translation file 
/share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt
pass 1: 7 segments changed
pass 2: 0 segments changed
writing annotation to s111_bla_8mm_orig2_annot.annot...
computing statistics for each annotation in 
/data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/label/lh.s111_bla_8mm_orig2_annot.annot.
reading volume /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/wm.mgz...
reading input surface 
/data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white...
reading input pial surface 
/data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.pial...
reading input white surface 
/data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white...
CTABfindAnnotation: ct was NULL
./targetAnnotStats.sh: line 21:  5086 Segmentation fault      (core dumped) 
mris_anatomical_stats -a ${SUBJECTS_DIR}/${sub}/label/lh.${targ}_annot.annot -b 
${sub} lh



./targetAnnotStats.sh: line 21:  4934 Segmentation fault      (core dumped) 
mris_anatomical_stats -a ${SUBJECTS_DIR}/${sub}/label/lh.${targ}_annot.annot -b 
${sub} lh >> log.txt 2>&1
reading parcellation volume from 
/data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/s111_bla_8mm_orig2.nii.gz...
reading input surface 
/data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white...
could not open translation file 
/share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt
pass 1: 7 segments changed
pass 2: 0 segments changed
writing annotation to s111_bla_8mm_orig2_annot.annot...
computing statistics for each annotation in 
/data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/label/lh.s111_bla_8mm_orig2_annot.annot.
reading volume /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/wm.mgz...
reading input surface 
/data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white...
reading input pial surface 
/data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.pial...
reading input white surface 
/data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white...
CTABfindAnnotation: ct was NULL
./targetAnnotStats.sh: line 21:  5086 Segmentation fault      (core dumped) 
mris_anatomical_stats -a ${SUBJECTS_DIR}/${sub}/label/lh.${targ}_annot.annot -b 
${sub} lh

Attachment: targetAnnotStats.sh
Description: Binary data



> On Apr 26, 2017, at 3:52 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
> 
> Hi Jared
> 
> can you send us the full command line and screen output?
> 
> cheers
> Bruce
> On Wed, 26 Apr 2017, Jared P Zimmerman wrote:
> 
>> Any chance I could get some help on this?  still having this problem
>> 
>>      On Apr 20, 2017, at 6:26 PM, Jared P Zimmerman
>>      <jar...@mail.med.upenn.edu> wrote:
>> Hi FS Experts,
>> I’m having trouble getting anatomical stats from a parcellation I made
>> out of scanner-space volume ROIs.  I have taken the following steps to
>> do this.
>> 
>> 1. mri_vol2vol --mov myROI.nii.gz --targ orig.mgz --regheader --o
>>    myROI_orig.nii.gz --interp nearest
>> 2. mris_sample_parc Subj111 lh myROI_orig.nii.gz myROIs.annot -ct
>>    ROI_test_table.txt 
>>     1. On this step I ALWAYS get an error “could not open translation
>>        file /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt”
>>        even though I specify a CT with -ct, or when I specify a table
>>        with -t, or with both
>>     2. This seems to work though and I can view this annot on the
>>        surface with tksurfer
>> 3. mris_anatomical_stats -a /path/to/myROIs.annot -b Subj111 lh
>> When I run mris_anatomical_stats I get the following error: 
>> CTABfindAnnotation: ct was NULL
>> Segmentation fault (core dumped)
>> I’m guessing this is from the color-table not being embedded in the
>> annot file, but I’ve tried to get that embedded in many ways.  
>> My questions are:
>> 
>> 1. What is causing the error with mris_anatomical_stats?
>> 2. What is the difference between the -t and -ct flags for
>>    mris_sample_parc and which should I use?
>> 3. Should I use a specific color-table for this?  I made my own which
>>    was just a space delimited file with “index name r g b a” for all
>>    my ROIs, but should I be adding this data to some existing
>>    color-table to make this work?
>> Thanks,
>> Jared
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