On Wed, Oct 31, 2012 at 9:31 AM, Christine Smith <cnsmith@ucsd.edu> wrote:

The command line was: recon-all -make -s CON1

I am not sure why the log said it was: recon-all -s
/usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel

I am running it again right now and it said the command line was:
recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1
-careg -careginv

It seems to be running through the processing stream. I will let you
know what it says after it finishes sometime tomorrow.

Christine

On Tue, Oct 30, 2012 at 6:13 PM, Bruce Fischl

<fischl@nmr.mgh.harvard.edu> wrote:
> so your recon-all command line was:
>
> recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel
>
> usually -s just takes the subject name/identifier, not the whole path, and
> why are you only rerunning calabel? I don't see what the error is, but this
> is an unusual usage
>
>
>
>
> On Tue, 30 Oct 2012, Christine Smith wrote:
>
>> See my original post at the end of this message and some more
>> information included below.
>>
>> What would have been edited between the previous run without errors
>> and the current run with errors is the brainmask, the wm.mgz file, and
>> control points.
>>
>> On Tue, Oct 30, 2012 at 1:21 PM, Christine Smith <cnsmith@ucsd.edu> wrote:
>>>
>>> Here it is:
>>>
>>> New invocation of recon-all
>>>
>>> Thu Oct 4 03:52:22 PDT 2012
>>> /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1
>>> /usr/local/freesurfer/bin/recon-all
>>> -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel
>>> #--------------------------------------
>>> #@# SubCort Seg Thu Oct 4 03:52:22 PDT 2012
>>>
>>> mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff
>>> aseg.manedit.mgz
>>>
>>> Linux squirelab.ucsd.edu 2.6.18-308.13.1.el5 #1 SMP Tue Aug 21
>>> 18:44:22 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> recon-all -s CON1 exited with ERRORS at Thu Oct 4 03:52:22 PDT 2012
>>>
>>> On Tue, Oct 30, 2012 at 12:45 PM, Bruce Fischl
>>> <fischl@nmr.mgh.harvard.edu> wrote:
>>>>
>>>> what were the last 20 lines or so of the recon-all.log?
>>>>
>>>> On Tue, 30 Oct 2012, Christine Smith wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> After successfully running a subject through freesurfer (recon-all
>>>>> -make all) several times as I fixed some pial and white matter edits,
>>>>> I now get the message that recon-all finished with errors. Inspection
>>>>> of the recon-all.log doesn't reveal any error messages to me in any
>>>>> particular step.
>>>>>
>>>>> What should I be looking for to track down the reason that errors were
>>>>> generated?
>>>>>
>>>>> I already examined the talairach transform and that looks great.
>>>>> I loaded the pial and white matter surfaces and they look fine. The
>>>>> segmentation aparc+aseg looks great too.
>>>>>
>>>>> Thanks,
>>>>> Christine
>>>>>
>>>>>
>>>>
>> _______________________________________________
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
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--
Christine N. Smith, Ph.D.
Department of Psychiatry
University of California, San Diego

--
Christine N. Smith, Ph.D.
Department of Psychiatry
University of California, San Diego