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
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.
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.
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.
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.
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.
- 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
- 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? 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.
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.
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.
- 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
- 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? 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.
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
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.
- 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
- 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? 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.
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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.
- 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
- 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? 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.
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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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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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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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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 . 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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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 . 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. > > _______________________________________________ > 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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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 . 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. >> >> _______________________________________________ >> 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks Bruce, this did it.
-jared
On May 4, 2017, at 12:33 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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 . 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. >>> >>> _______________________________________________ >>> 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 >> >> > _______________________________________________ > 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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Bruce Fischl -
Jared P Zimmerman