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> 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>> 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>> 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
>
>
>
> _______________________________________________
> Freesurfer mailing list

> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>

> 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 e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer