fwiw, this problem persists in FS6.0
-jared
On May 4, 2017, at 12:11 PM, Jared P Zimmerman jaredz@mail.med.upenn.edu wrote:
That’s what I did below, see the script and log.txt attached to a previous email. This is the output from the mris_sample_parc step
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…
Thanks, Jared
On May 4, 2017, at 11:36 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you try it with -ct <color table file>
and send us the output if that doesn't work? That's what we use internally cheers Bruce On Thu, 4 May 2017, Jared P Zimmerman wrote:
Yeah I see that, but the cma_parcellation_colors.txt isn’t distributed with FS 5.3, yet it is the default LUT called by mris_sample_parc. Also, I tried to use my own color table using the -ct flag but it continues to try to embed the cma_parcellation_colors.txt regardless of the LUT I put there.
Also, mris_sample_parc seems to work. I can visualize the parcellation that comes out of that fine, however it’s clear there’s no LUT embedded because the label names are wrong (see attached image).
I don’t care too much if the LUT is embedded properly, I just want to use the parcellation to get anatomical data about my regions, but mris_anatomical_stats seems to fail because the LUT isn’t embedded. I’m still confused about why the -ct flag in mris_sample_parc doesn’t seem to work.
Thanks, Jared
On May 4, 2017, at 10:58 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jared
it looks like it couldn't find the lookup tbale:
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
cheers Bruce On Thu, 4 May 2017, Jared P Zimmerman wrote:
Hey Bruce et al, any update on this?
Thanks, Jared
On Apr 28, 2017, at 2:48 PM, Jared P Zimmerman jaredz@mail.med.upenn.edu wrote:
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
<log.txt><targetAnnotStats.sh>
> 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. >> >> 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 >> _______________________________________________ >> 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. > _______________________________________________ > 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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