Thanks Bruce, this did it.
-jared
> On May 4, 2017, at 12:33 PM, Bruce Fischl <fis...@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 <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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