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
>>>>>>>>> _______________________________________________
>>>>>>>>> Freesurfer mailing list
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>>>>>>>>> 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
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>>>>>>>>> contains patient information, please contact the Partners Compliance
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>>>>>>>>
>>>>>>>>
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>>>>>>
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