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> 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>> 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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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