Re: [Freesurfer] error while running autorecon1 and autorecon2 in fs-v5.3
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//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 gr...@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: 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 zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@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 mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@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 mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@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:
Re: [Freesurfer] error while running autorecon1 and autorecon2 in fs-v5.3
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 gr...@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//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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@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/**freesur...@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 zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.**harvard.eduzkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.**harvard.eduzkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.**harvard.edu zkauf...@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 mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com wrote: ps: i believe my error is the same as the one in this thread: http://www.mail-archive.com/**freesur...@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 mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@gmail.com mailto:mpsam...@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
[Freesurfer] error while running autorecon1 and autorecon2 in fs-v5.3
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.
Re: [Freesurfer] error while running autorecon1 and autorecon2 in fs-v5.3
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 mpsam...@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.
Re: [Freesurfer] error while running autorecon1 and autorecon2 in fs-v5.3
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 mpsam...@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 mpsam...@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. ___ 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.
Re: [Freesurfer] error while running autorecon1 and autorecon2 in fs-v5.3
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 mpsam...@gmail.com mailto:mpsam...@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 mpsam...@gmail.com mailto:mpsam...@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
