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 <fis...@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 <fis...@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 <fis...@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 <jar...@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 <fis...@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
<jar...@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
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