Re: [Freesurfer] recon-all error: Correcting defect
External Email - Use Caution Dear Bram, Thanks for your help, yes I tried to fix this issue following Bruce´s suggestions and everything worked fine. I manually filled the brain lesions in the wm.mgz and now the recon-all did not stop in the correcting defect. Best regards, El lun., 8 jul. 2019 a las 17:17, Diamond, Bram Ryder (< brdiam...@mgh.harvard.edu>) escribió: > Hi Miguel! > > I'll be happy to help with your issue, but I'm having trouble finding your > subject's directory on our server. Could you please try and upload the data > via FTP, again? Also, have you tried either of Bruce's suggestions? > > Thanks, > Bram > > Bram R. Diamond, BSc > Research Technician II > Laboratory for Computational Neuroimaging > Martinos Center for Biomedical Imaging > Massachusetts General Hospital > 149 13th Street > Charlestown, MA 02129 > (p): 617-726-6598 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas > Fernández > Sent: Wednesday, June 26, 2019 11:37 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all error: Correcting defect > > External Email - Use Caution > > Hello Bruce, > > Ok, I have sent to you the subject via FileDrop if you want to take a > look. Thanks. > > Best regards, > > El mié., 26 jun. 2019 a las 17:04, Bruce Fischl (< > fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>) escribió: > Hi Miguel > > depending on the lesions it may not be fixable (since they may change the > topology of the cortex). If you upload the subject we will take a look, or > you can try manually filling in the lesion in the wm.mgz (or marking it as > lesion in the aseg.mgz) and seeing if that helps > > cheers > Bruce > On Wed, 26 Jun 2019, Miguel Ángel Rivas > Fernández wrote: > > > > > External Email - Use Caution > > > > > > I ran the recon-all in one subject and and this process was stopped in > the topology correction. In > > particular during the > > > > "CORRECTING DEFECT 36 (vertices=19847, convex hull=5892, v0=94733)". > > > > I reviewed the lh.inflated.nofix and the lh.orig.nofix files in Freeview > and I noticed that the this > > error would be located in the lh.inflated.nofix file. I am not > completely sure but I suspect that > > this error may be due to the fact that there is a large amount of brain > lesion and this would > > difficult the topology correction. How can I fix this problem? > > > > Thanks in advance. > > > > Best regards, > > > > -- > > Miguel Ángel Rivas Fernández > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Miguel Ángel Rivas Fernández > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all error: Correcting defect
Hi Miguel! I'll be happy to help with your issue, but I'm having trouble finding your subject's directory on our server. Could you please try and upload the data via FTP, again? Also, have you tried either of Bruce's suggestions? Thanks, Bram Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Miguel Ángel Rivas Fernández Sent: Wednesday, June 26, 2019 11:37 AM To: Freesurfer support list Subject: Re: [Freesurfer] recon-all error: Correcting defect External Email - Use Caution Hello Bruce, Ok, I have sent to you the subject via FileDrop if you want to take a look. Thanks. Best regards, El mié., 26 jun. 2019 a las 17:04, Bruce Fischl (mailto:fis...@nmr.mgh.harvard.edu>>) escribió: Hi Miguel depending on the lesions it may not be fixable (since they may change the topology of the cortex). If you upload the subject we will take a look, or you can try manually filling in the lesion in the wm.mgz (or marking it as lesion in the aseg.mgz) and seeing if that helps cheers Bruce On Wed, 26 Jun 2019, Miguel Ángel Rivas Fernández wrote: > > External Email - Use Caution > > > I ran the recon-all in one subject and and this process was stopped in the > topology correction. In > particular during the > > "CORRECTING DEFECT 36 (vertices=19847, convex hull=5892, v0=94733)". > > I reviewed the lh.inflated.nofix and the lh.orig.nofix files in Freeview and > I noticed that the this > error would be located in the lh.inflated.nofix file. I am not completely > sure but I suspect that > this error may be due to the fact that there is a large amount of brain > lesion and this would > difficult the topology correction. How can I fix this problem? > > Thanks in advance. > > Best regards, > > -- > Miguel Ángel Rivas Fernández > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Miguel Ángel Rivas Fernández ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all error: Correcting defect
External Email - Use Caution Hello Bruce, Ok, I have sent to you the subject via FileDrop if you want to take a look. Thanks. Best regards, El mié., 26 jun. 2019 a las 17:04, Bruce Fischl () escribió: > Hi Miguel > > depending on the lesions it may not be fixable (since they may change the > topology of the cortex). If you upload the subject we will take a look, or > you can try manually filling in the lesion in the wm.mgz (or marking it as > lesion in the aseg.mgz) and seeing if that helps > > cheers > Bruce > On Wed, 26 Jun 2019, Miguel Ángel Rivas > Fernández wrote: > > > > > External Email - Use Caution > > > > > > I ran the recon-all in one subject and and this process was stopped > in the topology correction. In > > particular during the > > > > "CORRECTING DEFECT 36 (vertices=19847, convex hull=5892, v0=94733)". > > > > I reviewed the lh.inflated.nofix and the lh.orig.nofix files in Freeview > and I noticed that the this > > error would be located in the lh.inflated.nofix file. I am not > completely sure but I suspect that > > this error may be due to the fact that there is a large amount of brain > lesion and this would > > difficult the topology correction. How can I fix this problem? > > > > Thanks in advance. > > > > Best regards, > > > > -- > > Miguel Ángel Rivas Fernández > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all error: Correcting defect
Hi Miguel depending on the lesions it may not be fixable (since they may change the topology of the cortex). If you upload the subject we will take a look, or you can try manually filling in the lesion in the wm.mgz (or marking it as lesion in the aseg.mgz) and seeing if that helps cheers Bruce On Wed, 26 Jun 2019, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution I ran the recon-all in one subject and and this process was stopped in the topology correction. In particular during the "CORRECTING DEFECT 36 (vertices=19847, convex hull=5892, v0=94733)". I reviewed the lh.inflated.nofix and the lh.orig.nofix files in Freeview and I noticed that the this error would be located in the lh.inflated.nofix file. I am not completely sure but I suspect that this error may be due to the fact that there is a large amount of brain lesion and this would difficult the topology correction. How can I fix this problem? Thanks in advance. Best regards, -- Miguel Ángel Rivas Fernández ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all error: Correcting Defect 2
v5.0.0 On May 16, 2013, at 2:18 PM, Bruce Fischl wrote: Hi Sudhin what FS version are you running? Bruce On Thu, 16 May 2013, Sudhin A. Shah wrote: Hi, I got the following error: CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Thanks, S ___ 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
[Freesurfer] recon-all error: Correcting Defect 2
Hi, I got the following error: CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Thanks, S ___ 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 error: Correcting Defect 2
Hi Sudhin what FS version are you running? Bruce On Thu, 16 May 2013, Sudhin A. Shah wrote: Hi, I got the following error: CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Thanks, S ___ 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.
