Oh, I see it would prevent us from getting the aseg.stats file. 
That's not good; we want the whole enchilada :-)

Never mind; will follow your previous suggestion and run recon-all all the way through; 
Thanks Doug; 

Mehul




On Tue, Jun 4, 2013 at 11:41 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

It would stop the error but still prevent you from getting the stats file. If you don't need the stats file, you can add -nosegstats to the cmd line as the last option.
doug



On 06/04/2013 02:32 PM, Mehul Sampat wrote:
Hi Doug,

Thanks; Will do so.

Also I forgot to mention one thing in the previous email:

for case -autorecon3, also there is:
set DoSegStats   = 1; (in recon-all script in 5.3 this is line 5526)

would it help, if  "set DoSegStats       = 1" was used only in -autorecon3 and not in the
-autorecon2 or -autorecon2-cp ? or would this break other stuff.

Mehul





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

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        <tel:617-726-7422>>

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    --     Douglas N. Greve, Ph.D.
    MGH-NMR Center
    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    Phone Number: 617-724-2358 <tel:617-724-2358>
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