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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