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
On Apr 26, 2017, at 3:52 PM, Bruce Fischl fischl@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 <jaredz@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.
- mri_vol2vol --mov myROI.nii.gz --targ orig.mgz --regheader --o myROI_orig.nii.gz --interp nearest
- mris_sample_parc Subj111 lh myROI_orig.nii.gz myROIs.annot -ct ROI_test_table.txt
- 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
- This seems to work though and I can view this annot on the surface with tksurfer
- 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:
- What is causing the error with mris_anatomical_stats?
- What is the difference between the -t and -ct flags for mris_sample_parc and which should I use?
- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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