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 <fis...@nmr.mgh.harvard.edu>: > 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 <fis...@nmr.mgh.harvard.edu>: >> 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 >> <fis...@nmr.mgh.harvard.edu>: >> 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. > >
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