Re: [Freesurfer] Recon-all get stucked without error during processing
try specifying -no-wsgcaatlas or -no-wsatlas and rerunning just the skull stripping and see if it fixes things cheers Bruce On Thu, 7 Jan 2016, Matthieu Vanhoutte wrote: Hi Bruce, This problem isn't resolved yet. I uploaded the subject raw 3D T1 on FileDrop. Changing the watershed parameters could be done in the recon-all command ? Thanks in advance ! Best regards, Matthieu 2016-01-07 14:58 GMT+01:00 Bruce Fischl : Hi Matthieu was this ever resolved? If not, you can upload the subject and we will take a look. You could also try messing with the watershed parameters (starting with changing the preflooding height to me more aggressive). cheers Bruce On Thu, 10 Dec 2015, Matthieu Vanhoutte wrote: Hi Bruce, Do you have an idea of how to solve this problem of skull stripping (below) ? Best regards, Matthieu 2015-12-09 16:25 GMT+01:00 Matthieu Vanhoutte : Hi Bruce, In fact T1.mgz is ok, but the skull stripping failed and seemed to have taken only the jawbone and the neck. Best regards, Matthieu 2015-12-09 16:16 GMT+01:00 Bruce Fischl : Hi Matthieu you need to track backwards and see where the problem started. Why is the norm warped? Actaully, it shouldn't be warped, although it might be truncated if the skull stripping failed. cheers Bruce On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote: Hi Bruce, Indeed norm.mgz isn't empty but doesn't look well (truncated and warped). Is this bug fixed in the v6 beta release ? If this is the case : 1) Would you advise me to try on the v6 ? 2) Should I so relaunch all recon-all process on my subjects computed with v5.3 and work only with the v6 beta ? Best regards, Matthieu 2015-12-09 15:55 GMT+01:00 Bruce Fischl : Hi Matthieu this might be a bug that is fixed in 6.0. Can you cehck the input to mri_cc (norm.mgz) and make sure it is not empty? In older versions if the skull stripping failed and generated an empty norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang. cheers Bruce On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote: > Dear FS epxerts, > > I have launched a recon-all process on a subject. Unfortunately, I tried two times but the process get stucked at the same step > without error. > > Please found the recon-all.log associated attached to this mail. > > Thanks in advance for helping ! > > Best regards, > Matthieu > > ___ 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
Re: [Freesurfer] Recon-all get stucked without error during processing
Hi Bruce, This problem isn't resolved yet. I uploaded the subject raw 3D T1 on FileDrop. Changing the watershed parameters could be done in the recon-all command ? Thanks in advance ! Best regards, Matthieu 2016-01-07 14:58 GMT+01:00 Bruce Fischl : > Hi Matthieu > > was this ever resolved? If not, you can upload the subject and we will > take a look. You could also try messing with the watershed parameters > (starting with changing the preflooding height to me more aggressive). > > cheers > Bruce > > > > On Thu, 10 Dec 2015, Matthieu Vanhoutte wrote: > > Hi Bruce, >> >> Do you have an idea of how to solve this problem of skull stripping >> (below) >> ? >> >> Best regards, >> Matthieu >> >> 2015-12-09 16:25 GMT+01:00 Matthieu Vanhoutte < >> matthieuvanhou...@gmail.com>: >> Hi Bruce, >> >> In fact T1.mgz is ok, but the skull stripping failed and seemed to >> have taken only the jawbone and the neck. >> >> Best regards, >> Matthieu >> >> 2015-12-09 16:16 GMT+01:00 Bruce Fischl : >> Hi Matthieu >> >> you need to track backwards and see where the problem >> started. Why is the norm warped? Actaully, it shouldn't be >> warped, although it might be truncated if the skull >> stripping failed. >> >> cheers >> Bruce >> On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote: >> >> Hi Bruce, >> >> Indeed norm.mgz isn't empty but doesn't look >> well (truncated and warped). >> >> Is this bug fixed in the v6 beta release ? >> >> If this is the case : >> 1) Would you advise me to try on the v6 ? >> 2) Should I so relaunch all recon-all process >> on my subjects computed with v5.3 and work >> only with the v6 beta ? >> >> Best regards, >> Matthieu >> >> 2015-12-09 15:55 GMT+01:00 Bruce Fischl >> : >> Hi Matthieu >> >> this might be a bug that is fixed in >> 6.0. Can you cehck the input to >> mri_cc (norm.mgz) and make sure it is >> not empty? In older versions if the >> skull stripping failed and generated an >> empty >> norm.mgz/aseg.auto_noCCseg.mgz the >> mri_cc code would hang. >> >> cheers >> Bruce >> >> On Wed, 9 Dec 2015, >> Matthieu Vanhoutte wrote: >> >> > Dear FS epxerts, >> > >> > I have launched a recon-all process on >> a subject. Unfortunately, I tried two times >> but the process get stucked at >> the same step >> > without error. >> > >> > Please found the recon-all.log >> associated attached to this mail. >> > >> > Thanks in advance for helping ! >> > >> > Best regards, >> > Matthieu >> > >> > >> ___ >> 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. >> >> >> >> >> > ___ > 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 c
Re: [Freesurfer] Recon-all get stucked without error during processing
Hi Bruce, Do you have an idea of how to solve this problem of skull stripping (below) ? Best regards, Matthieu 2015-12-09 16:25 GMT+01:00 Matthieu Vanhoutte : > Hi Bruce, > > In fact T1.mgz is ok, but the skull stripping failed and seemed to have > taken only the jawbone and the neck. > > Best regards, > Matthieu > > > 2015-12-09 16:16 GMT+01:00 Bruce Fischl : > >> Hi Matthieu >> >> you need to track backwards and see where the problem started. Why is the >> norm warped? Actaully, it shouldn't be warped, although it might be >> truncated if the skull stripping failed. >> >> >> cheers >> Bruce >> On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote: >> >> Hi Bruce, >>> >>> Indeed norm.mgz isn't empty but doesn't look well (truncated and warped). >>> >>> Is this bug fixed in the v6 beta release ? >>> >>> If this is the case : >>> 1) Would you advise me to try on the v6 ? >>> 2) Should I so relaunch all recon-all process on my subjects computed >>> with v5.3 and work only with the v6 beta ? >>> >>> Best regards, >>> Matthieu >>> >>> 2015-12-09 15:55 GMT+01:00 Bruce Fischl : >>> Hi Matthieu >>> >>> this might be a bug that is fixed in 6.0. Can you cehck the input >>> to >>> mri_cc (norm.mgz) and make sure it is not empty? In older versions >>> if the >>> skull stripping failed and generated an empty >>> norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang. >>> >>> cheers >>> Bruce >>> >>> On Wed, 9 Dec 2015, >>> Matthieu Vanhoutte wrote: >>> >>> > Dear FS epxerts, >>> > >>> > I have launched a recon-all process on a subject. Unfortunately, >>> I tried two times but the process get stucked at >>> the same step >>> > without error. >>> > >>> > Please found the recon-all.log associated attached to this mail. >>> > >>> > Thanks in advance for helping ! >>> > >>> > Best regards, >>> > Matthieu >>> > >>> > >>> ___ >>> 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. >> >> > ___ 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] Recon-all get stucked without error during processing
Hi Bruce, In fact T1.mgz is ok, but the skull stripping failed and seemed to have taken only the jawbone and the neck. Best regards, Matthieu 2015-12-09 16:16 GMT+01:00 Bruce Fischl : > Hi Matthieu > > you need to track backwards and see where the problem started. Why is the > norm warped? Actaully, it shouldn't be warped, although it might be > truncated if the skull stripping failed. > > > cheers > Bruce > On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote: > > Hi Bruce, >> >> Indeed norm.mgz isn't empty but doesn't look well (truncated and warped). >> >> Is this bug fixed in the v6 beta release ? >> >> If this is the case : >> 1) Would you advise me to try on the v6 ? >> 2) Should I so relaunch all recon-all process on my subjects computed >> with v5.3 and work only with the v6 beta ? >> >> Best regards, >> Matthieu >> >> 2015-12-09 15:55 GMT+01:00 Bruce Fischl : >> Hi Matthieu >> >> this might be a bug that is fixed in 6.0. Can you cehck the input to >> mri_cc (norm.mgz) and make sure it is not empty? In older versions >> if the >> skull stripping failed and generated an empty >> norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang. >> >> cheers >> Bruce >> >> On Wed, 9 Dec 2015, >> Matthieu Vanhoutte wrote: >> >> > Dear FS epxerts, >> > >> > I have launched a recon-all process on a subject. Unfortunately, >> I tried two times but the process get stucked at >> the same step >> > without error. >> > >> > Please found the recon-all.log associated attached to this mail. >> > >> > Thanks in advance for helping ! >> > >> > Best regards, >> > Matthieu >> > >> > >> ___ >> 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. > > ___ 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] Recon-all get stucked without error during processing
Hi Matthieu you need to track backwards and see where the problem started. Why is the norm warped? Actaully, it shouldn't be warped, although it might be truncated if the skull stripping failed. cheers Bruce On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote: Hi Bruce, Indeed norm.mgz isn't empty but doesn't look well (truncated and warped). Is this bug fixed in the v6 beta release ? If this is the case : 1) Would you advise me to try on the v6 ? 2) Should I so relaunch all recon-all process on my subjects computed with v5.3 and work only with the v6 beta ? Best regards, Matthieu 2015-12-09 15:55 GMT+01:00 Bruce Fischl : Hi Matthieu this might be a bug that is fixed in 6.0. Can you cehck the input to mri_cc (norm.mgz) and make sure it is not empty? In older versions if the skull stripping failed and generated an empty norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang. cheers Bruce On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote: > Dear FS epxerts, > > I have launched a recon-all process on a subject. Unfortunately, I tried two times but the process get stucked at the same step > without error. > > Please found the recon-all.log associated attached to this mail. > > Thanks in advance for helping ! > > Best regards, > Matthieu > > ___ 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] Recon-all get stucked without error during processing
Hi Bruce, Indeed norm.mgz isn't empty but doesn't look well (truncated and warped). Is this bug fixed in the v6 beta release ? If this is the case : 1) Would you advise me to try on the v6 ? 2) Should I so relaunch all recon-all process on my subjects computed with v5.3 and work only with the v6 beta ? Best regards, Matthieu 2015-12-09 15:55 GMT+01:00 Bruce Fischl : > Hi Matthieu > > this might be a bug that is fixed in 6.0. Can you cehck the input to > mri_cc (norm.mgz) and make sure it is not empty? In older versions if the > skull stripping failed and generated an empty > norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang. > > cheers > Bruce > > On Wed, 9 Dec 2015, > Matthieu Vanhoutte wrote: > > > Dear FS epxerts, > > > > I have launched a recon-all process on a subject. Unfortunately, I tried > two times but the process get stucked at the same step > > without error. > > > > Please found the recon-all.log associated attached to this mail. > > > > Thanks in advance for helping ! > > > > Best regards, > > Matthieu > > > > > ___ > 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] Recon-all get stucked without error during processing
Hi Matthieu this might be a bug that is fixed in 6.0. Can you cehck the input to mri_cc (norm.mgz) and make sure it is not empty? In older versions if the skull stripping failed and generated an empty norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang. cheers Bruce On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote: > Dear FS epxerts, > > I have launched a recon-all process on a subject. Unfortunately, I tried two > times but the process get stucked at the same step > without error. > > Please found the recon-all.log associated attached to this mail. > > Thanks in advance for helping ! > > Best regards, > Matthieu > > ___ 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.
