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
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 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
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 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 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 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.
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
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
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:
- run recon-all with -all
- add control points if required
- run recon-all with -autorecon2-cp and autorecon3
This ran through without any errors;
Now to save some processing time, the modified workflow is:
- run recon-all with -autorecon1 -autorecon2
- add control points if required
- 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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
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.eduwrote:
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:
- run recon-all with -all
- add control points if required
- run recon-all with -autorecon2-cp and autorecon3
This ran through without any errors;
Now to save some processing time, the modified workflow is:
- run recon-all with -autorecon1 -autorecon2
- add control points if required
- 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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> <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 > > > > > > 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/**compliancelinehttp://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 <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
> <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
<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.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.eduwrote:
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.**edugreve@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<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <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.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>> <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> <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>> > > <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.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>> > > <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 > > > > > > > > ______________________________**_________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><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> > > > > > > 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<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 <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><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.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><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
<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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting><http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html><http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><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> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Gennan Chen -
Mehul Sampat -
Z K