On Tue, Jun 4, 2013 at 11:24 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

this is a bug in mri_segstats. For now, you will need to run recon-all to the end to generate the ribbon.mgz file
doug

On 06/04/2013 02:12 PM, Mehul Sampat wrote:

Hi Doug,
Yes, we see the same error as in msg28047.html; here is the line from my recon-all.log:

mghRead(/mnt/horizon/stage/HLC/9999/004_151_3106223/WBS/Baseline/Freesurfer/mri/ribbon.mgz, -1): could not open file

In msg28047.html, Milkos suggested that the issue could be the following line in recon-all
" set DoSegStats = 1"

(in recon-all script in 5.2 this is line 5225; under the case "-autorecon2" )
(in recon-all script in 5.3 this is line 5401; under the case "-autorecon2" )

I think he is right; first i was confused why this issue was not seen with -autrecon2-cp

because there is " set DoSegStats = 1" for -autrecon2-cp too;
(in recon-all script in 5.3 this is line 5480; under the case "-autorecon2-cp")

But normally we run -autorecon3 or -all before running -autorecon2-cp; so in this case
the ribbon exists and the error does not show up with -autorecon2-cp (if -all or -autorecon3 is run before).

Mehul

On Tue, Jun 4, 2013 at 10:49 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

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>

> <mailto: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>>
> > <mailto: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>>
> > <mailto: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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Douglas N. Greve, Ph.D.
MGH-NMR Center
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MGH-NMR Center
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