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.eduwrote:
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.**edugreve@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.htmlhttp://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<zkaufman@nmr.mgh.harvard.edu>> <mailto:zkaufman@nmr.mgh.**harvard.edu<zkaufman@nmr.mgh.harvard.edu> <mailto:zkaufman@nmr.mgh.**harvard.edu <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.htmlhttp://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 > > > > > > > > ______________________________**_________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
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> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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