I see. This is the problem - mris_sample_parc is one of the binaries that requires all options come before the mandatory arguments. Move the -ct <ctab> part to the beginning and it should work
cheers Bruce On Thu, 4 May 2017, Jared P Zimmerman wrote:
mris_sample_parc ${sub} \ lh ${targ}.nii.gz \ ${targ}_fs6_annot.annot \ -ct ${SUBJECTS_DIR}/${sub}/bla_test_table.txt
This is the call from my script, which didn’t get written to stdout. The bla_test_table.txt exists, and is just a space delimited file with “index name r g b a” for each label. I’ve also tried pointing the -ct flag to a LUT that exists in $FREESURFER_HOME and is distributed with FS, e.g. ASegStatsLUT.txt or FreeSurferColorLUT.txt with no success, i.e. below.
mris_sample_parc Subj111 lh s111_bla_8mm_orig2.nii.gz s111_bla_8mm_orig2_v2_annot.annot -ct AsegStatsLUT.txt 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... pass 1: 7 segments changed pass 2: 0 segments changed could not open translation file /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt writing annotation to s111_bla_8mm_orig2_v2_annot.annot…
Thanks, Jared
On May 4, 2017, at 12:15 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
sorry, I don't see the mris_sample_parc command line. Can you just send it and the entire screen output? On Thu, 4 May 2017, Jared P Zimmerman 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 . 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