Re: [Freesurfer] error while running autorecon1 and autorecon2 in fs-v5.3

The error in msg28047.html is that there was no ribbon.mgz. Is that the error you are receiving? http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html On 06/04/2013 01:45 PM, Mehul Sampat wrote:

Hi Zeke, Thanks for looking into this; had a quick followup item to report. So for the same subject "recon-all -all" runs through smoothly; (it was only recon-all -autorecon1 -autorecon2 that generated the error)

I had not seen the error before since in the past, my workflow was as follows:

1. run recon-all with -all
2. add control points if required
3. run recon-all with -autorecon2-cp and autorecon3

This ran through without any errors;

Now to save some processing time, the modified workflow is:

1. run recon-all with -autorecon1 -autorecon2
2. add control points if required
3. run recon-all with -autorecon2-cp and autorecon3

(It was step 1 in this modified workflow that generated the issue)

Mehul ps: the recon-all.log file from the error reported earlier is attached for reference (i sent it to you but forgot to send it to the mailing list earlier)

On Thu, May 30, 2013 at 8:31 AM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:

Could you provide the recon-all.log file?

-Zeke

On 05/30/2013 10:24 AM, Gennan Chen wrote:
> Does 5.3 assume recon-all -all will always run first? Since
ribbon.mgz
> will not get created till autorecon3. In V4, that is part of
autorecon2
> though.
>
> Gen
>
>
> On Thu, May 30, 2013 at 12:24 AM, Mehul Sampat
<mpsampat@gmail.com <mailto:mpsampat@gmail.com>
> <mailto:mpsampat@gmail.com <mailto:mpsampat@gmail.com>>> wrote:
>
>     ps: i believe my error is the same as the one in this thread:
>
>
>
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html
>
>
>     Mehul
>
>
>     On Thu, May 30, 2013 at 12:13 AM, Mehul Sampat
<mpsampat@gmail.com <mailto:mpsampat@gmail.com>
>     <mailto:mpsampat@gmail.com <mailto:mpsampat@gmail.com>>> wrote:
>
>         Hi Folks,
>         I am running recon-all with -autorecon1
>         -autorecon2,  -nomotioncor -notal-check -nonuintensitycor
>         (this is with fs version 5.3)
>         it almost runs through but toward the end, when
mri_segstats is
>         called I get the error message:
>         .../mri/ribbon.mgz, -1): could not open file
>         any ideas why this could be occurring ?
>         Thanks
>         Mehul
>
>
>
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