Dear mailing list,
I am trying to batch a series of 30 MRI images using the following command: recon-all -autorecon2-cp -subjid ID001 -qcache
But for each image the process exits with the following errors: --------------------------------------------------- #@# 1/1 ID_001 Wed Aug 16 11:39:12 AEST 2017 -------------- ----------------------- mri_surf2surf --srcsubject ID_001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.18138/ID_001.1.mgh --sval /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = ID_001 srcval = /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.18138/ID_001.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.sphere.reg Loading source data Reading curvature file /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume ERROR: number of vertices in /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume does not match surface (109952,110385) ERROR: reading curvature file Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ID_001 exited with ERRORS at Wed Aug 16 11:39:13 AEST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I came across an earlier post in relation to a similar error (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.h... https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.html) where it was recommended that you run “recon-all -s subjid -make all” to rebuild all files where the dependency chain is wrong. I ran this for each of the subjects and then tried to rerun my original recon-all command again but got the same error. Do you have any alternate suggestions for fixing this problem?
Kind regards, Bronwyn Overs Research Assistant
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
neura.edu.au http://neura.edu.au/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe
That means that the surfaces are out of sync. the -make-all only works in certain circumstances. You can delete everything in the surf folder (it should all be recreated anyway with -autorecon2-cp)
On 08/15/2017 10:04 PM, Bronwyn Overs wrote:
Dear mailing list,
I am trying to batch a series of 30 MRI images using the following command: recon-all -autorecon2-cp -subjid ID001 -qcache
But for each image the process exits with the following errors:
#@# 1/1 ID_001 Wed Aug 16 11:39:12 AEST 2017 --------------
mri_surf2surf --srcsubject ID_001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.18138/ID_001.1.mgh --sval /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = ID_001 srcval = /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.18138/ID_001.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.sphere.reg Loading source data Reading curvature file /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume ERROR: number of vertices in /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume does not match surface (109952,110385) ERROR: reading curvature file Linux katana.neura.edu.au http://katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ID_001 exited with ERRORS at Wed Aug 16 11:39:13 AEST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I came across an earlier post in relation to a similar error (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.h...) where it was recommended that you run “recon-all -s subjid -make all” to rebuild all files where the dependency chain is wrong. I ran this for each of the subjects and then tried to rerun my original recon-all command again but got the same error. Do you have any alternate suggestions for fixing this problem?
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
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Hi Douglas,
Thanks for your reply. I followed your suggestion and deleted everything in the surf folder for each subject. I am not getting the following error:
Reading source surface reg /workingdata/ID_001/surf/lh.sphere.reg No such file or directory mri_surf2surf: could not read surface /workingdata/ID_001/surf/lh.sphere.reg No such file or directory Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ID_001 exited with ERRORS at Thu Aug 17 11:14:08 AEST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting%5C%5C
Should I try running the recon-all -all for each subject? Kind regards, Bronwyn Overs Research Assistant
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
neura.edu.au http://neura.edu.au/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe
On 17 Aug 2017, at 8:27 am, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
That means that the surfaces are out of sync. the -make-all only works in certain circumstances. You can delete everything in the surf folder (it should all be recreated anyway with -autorecon2-cp)
On 08/15/2017 10:04 PM, Bronwyn Overs wrote:
Dear mailing list,
I am trying to batch a series of 30 MRI images using the following command: recon-all -autorecon2-cp -subjid ID001 -qcache
But for each image the process exits with the following errors:
#@# 1/1 ID_001 Wed Aug 16 11:39:12 AEST 2017 --------------
mri_surf2surf --srcsubject ID_001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.18138/ID_001.1.mgh --sval /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = ID_001 srcval = /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.18138/ID_001.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.sphere.reg Loading source data Reading curvature file /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume ERROR: number of vertices in /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume does not match surface (109952,110385) ERROR: reading curvature file Linux katana.neura.edu.au http://katana.neura.edu.au/ <http://katana.neura.edu.au http://katana.neura.edu.au/> 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ID_001 exited with ERRORS at Wed Aug 16 11:39:13 AEST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I came across an earlier post in relation to a similar error (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.h... https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.html) where it was recommended that you run “recon-all -s subjid -make all” to rebuild all files where the dependency chain is wrong. I ran this for each of the subjects and then tried to rerun my original recon-all command again but got the same error. Do you have any alternate suggestions for fixing this problem?
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au/ <http://neura.edu.au http://neura.edu.au/>
Follow @neuraustralia on twitter <https://twitter.com/neuraustralia https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe http://www.neura.edu.au/help-research/subscribe>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 Phone Number: 617-724-2358 Fax: 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 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/ 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 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.
Hi Douglas,
Do you have any thoughts about the new missing directory error I am getting detailed below? Kind regards, Bronwyn Overs Research Assistant
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
neura.edu.au http://neura.edu.au/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe
On 17 Aug 2017, at 1:16 pm, Bronwyn Overs b.overs@neura.edu.au wrote:
Hi Douglas,
Thanks for your reply. I followed your suggestion and deleted everything in the surf folder for each subject. I am not getting the following error:
Reading source surface reg /workingdata/ID_001/surf/lh.sphere.reg No such file or directory mri_surf2surf: could not read surface /workingdata/ID_001/surf/lh.sphere.reg No such file or directory Linux katana.neura.edu.au http://katana.neura.edu.au/ 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ID_001 exited with ERRORS at Thu Aug 17 11:14:08 AEST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting%5C%5C
Should I try running the recon-all -all for each subject? Kind regards, Bronwyn Overs Research Assistant
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
neura.edu.au http://neura.edu.au/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe
On 17 Aug 2017, at 8:27 am, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That means that the surfaces are out of sync. the -make-all only works in certain circumstances. You can delete everything in the surf folder (it should all be recreated anyway with -autorecon2-cp)
On 08/15/2017 10:04 PM, Bronwyn Overs wrote:
Dear mailing list,
I am trying to batch a series of 30 MRI images using the following command: recon-all -autorecon2-cp -subjid ID001 -qcache
But for each image the process exits with the following errors:
#@# 1/1 ID_001 Wed Aug 16 11:39:12 AEST 2017 --------------
mri_surf2surf --srcsubject ID_001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.18138/ID_001.1.mgh --sval /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = ID_001 srcval = /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.18138/ID_001.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.sphere.reg Loading source data Reading curvature file /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume ERROR: number of vertices in /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume does not match surface (109952,110385) ERROR: reading curvature file Linux katana.neura.edu.au http://katana.neura.edu.au/ <http://katana.neura.edu.au http://katana.neura.edu.au/> 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ID_001 exited with ERRORS at Wed Aug 16 11:39:13 AEST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I came across an earlier post in relation to a similar error (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.h... https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.html) where it was recommended that you run “recon-all -s subjid -make all” to rebuild all files where the dependency chain is wrong. I ran this for each of the subjects and then tried to rerun my original recon-all command again but got the same error. Do you have any alternate suggestions for fixing this problem?
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au/ <http://neura.edu.au http://neura.edu.au/>
Follow @neuraustralia on twitter <https://twitter.com/neuraustralia https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe http://www.neura.edu.au/help-research/subscribe>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 Phone Number: 617-724-2358 Fax: 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 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/ 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 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 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.
Hi Bronwyn,
Doug is out of the office today. What is the command you ran after deleting everything in the surf folder? Can you send us the recon-all.log?
Best,
Emma
---------
Emma Boyd
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bronwyn Overs b.overs@neura.edu.au Sent: Thursday, August 24, 2017 9:14 PM To: Freesurfer support list Subject: Re: [Freesurfer] Recon-all error
Hi Douglas,
Do you have any thoughts about the new missing directory error I am getting detailed below?
Kind regards,
Bronwyn Overs Research Assistant
[Neuroscience Research Australia]
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
neura.edu.au http://neura.edu.au
[Follow @neuraustralia on twitter]https://twitter.com/neuraustralia[Follow NeuRA on facebook]https://www.facebook.com/NeuroscienceResearchAustralia[Subscribe to the NeuRA Magazine]http://www.neura.edu.au/help-research/subscribe
On 17 Aug 2017, at 1:16 pm, Bronwyn Overs <b.overs@neura.edu.aumailto:b.overs@neura.edu.au> wrote:
Hi Douglas,
Thanks for your reply. I followed your suggestion and deleted everything in the surf folder for each subject. I am not getting the following error:
Reading source surface reg /workingdata/ID_001/surf/lh.sphere.reg No such file or directory mri_surf2surf: could not read surface /workingdata/ID_001/surf/lh.sphere.reg No such file or directory Linux katana.neura.edu.auhttp://katana.neura.edu.au/ 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ID_001 exited with ERRORS at Thu Aug 17 11:14:08 AEST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting%5C%5C
Should I try running the recon-all -all for each subject?
Kind regards,
Bronwyn Overs Research Assistant
[Neuroscience Research Australia]
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
neura.edu.au http://neura.edu.au/
[Follow @neuraustralia on twitter]https://twitter.com/neuraustralia[Follow NeuRA on facebook]https://www.facebook.com/NeuroscienceResearchAustralia[Subscribe to the NeuRA Magazine]http://www.neura.edu.au/help-research/subscribe
On 17 Aug 2017, at 8:27 am, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
That means that the surfaces are out of sync. the -make-all only works in certain circumstances. You can delete everything in the surf folder (it should all be recreated anyway with -autorecon2-cp)
On 08/15/2017 10:04 PM, Bronwyn Overs wrote: Dear mailing list,
I am trying to batch a series of 30 MRI images using the following command: recon-all -autorecon2-cp -subjid ID001 -qcache
But for each image the process exits with the following errors: --------------------------------------------------- #@# 1/1 ID_001 Wed Aug 16 11:39:12 AEST 2017 -------------- ----------------------- mri_surf2surf --srcsubject ID_001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.18138/ID_001.1.mgh --sval /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = ID_001 srcval = /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.18138/ID_001.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.sphere.reg Loading source data Reading curvature file /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume ERROR: number of vertices in /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume does not match surface (109952,110385) ERROR: reading curvature file Linux katana.neura.edu.auhttp://katana.neura.edu.au/ <http://katana.neura.edu.auhttp://katana.neura.edu.au/> 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ID_001 exited with ERRORS at Wed Aug 16 11:39:13 AEST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I came across an earlier post in relation to a similar error (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.h...) where it was recommended that you run “recon-all -s subjid -make all” to rebuild all files where the dependency chain is wrong. I ran this for each of the subjects and then tried to rerun my original recon-all command again but got the same error. Do you have any alternate suggestions for fixing this problem?
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
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Hi Emma,
Thanks for your reply. I just tried running the recon-all process from the beginning using the -all flag and it seems to have fixed whatever the error was and the processing completed successfully. Kind regards, Bronwyn Overs Research Assistant
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
neura.edu.au http://neura.edu.au/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe
On 25 Aug 2017, at 11:11 pm, Boyd, Emma EBOYD2@mgh.harvard.edu wrote:
Hi Bronwyn,
Doug is out of the office today. What is the command you ran after deleting everything in the surf folder? Can you send us the recon-all.log?
Best, Emma
Emma Boyd Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bronwyn Overs b.overs@neura.edu.au Sent: Thursday, August 24, 2017 9:14 PM To: Freesurfer support list Subject: Re: [Freesurfer] Recon-all error
Hi Douglas,
Do you have any thoughts about the new missing directory error I am getting detailed below? Kind regards, Bronwyn Overs Research Assistant
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au http://neura.edu.au/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe
On 17 Aug 2017, at 1:16 pm, Bronwyn Overs <b.overs@neura.edu.au mailto:b.overs@neura.edu.au> wrote:
Hi Douglas,
Thanks for your reply. I followed your suggestion and deleted everything in the surf folder for each subject. I am not getting the following error:
Reading source surface reg /workingdata/ID_001/surf/lh.sphere.reg No such file or directory mri_surf2surf: could not read surface /workingdata/ID_001/surf/lh.sphere.reg No such file or directory Linux katana.neura.edu.au http://katana.neura.edu.au/ 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ID_001 exited with ERRORS at Thu Aug 17 11:14:08 AEST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting%5C%5C
Should I try running the recon-all -all for each subject? Kind regards, Bronwyn Overs Research Assistant
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au http://neura.edu.au/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe
On 17 Aug 2017, at 8:27 am, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That means that the surfaces are out of sync. the -make-all only works in certain circumstances. You can delete everything in the surf folder (it should all be recreated anyway with -autorecon2-cp)
On 08/15/2017 10:04 PM, Bronwyn Overs wrote:
Dear mailing list,
I am trying to batch a series of 30 MRI images using the following command: recon-all -autorecon2-cp -subjid ID001 -qcache
But for each image the process exits with the following errors:
#@# 1/1 ID_001 Wed Aug 16 11:39:12 AEST 2017 --------------
mri_surf2surf --srcsubject ID_001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.18138/ID_001.1.mgh --sval /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = ID_001 srcval = /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.18138/ID_001.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.sphere.reg Loading source data Reading curvature file /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume ERROR: number of vertices in /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume does not match surface (109952,110385) ERROR: reading curvature file Linux katana.neura.edu.au http://katana.neura.edu.au/ <http://katana.neura.edu.au http://katana.neura.edu.au/> 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ID_001 exited with ERRORS at Wed Aug 16 11:39:13 AEST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I came across an earlier post in relation to a similar error (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.h... https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.html) where it was recommended that you run “recon-all -s subjid -make all” to rebuild all files where the dependency chain is wrong. I ran this for each of the subjects and then tried to rerun my original recon-all command again but got the same error. Do you have any alternate suggestions for fixing this problem?
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au/ <http://neura.edu.au http://neura.edu.au/>
Follow @neuraustralia on twitter <https://twitter.com/neuraustralia https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe http://www.neura.edu.au/help-research/subscribe>
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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 Fax: 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 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/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Boyd, Emma -
Bronwyn Overs -
Douglas N Greve