fwiw, this problem persists in FS6.0 -jared
> On May 4, 2017, at 12:11 PM, Jared P Zimmerman <[email protected]> > 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 <[email protected]> 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 <[email protected]> >>>> 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 >>>>>> <[email protected]> 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 <[email protected]> >>>>>>> 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 >>>>>>>> <[email protected]> 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 >>>>>>>> [email protected] >>>>>>>> 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 >>>>>>> [email protected] >>>>>>> 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 >>>>>> [email protected] >>>>>> 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 >>>>> [email protected] >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> [email protected] >>>> 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 >> [email protected] >> 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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
