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,
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
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 (fischl@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 CautionI 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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Miguel Ángel Rivas Fernández miguelrivasfdez@gmail.com 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 (<fischl@nmr.mgh.harvard.edumailto:fischl@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 CautionI 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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Miguel Ángel Rivas Fernández
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 (< BRDIAMOND@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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas Fernández miguelrivasfdez@gmail.com Sent: Wednesday, June 26, 2019 11:37 AM To: Freesurfer support list Subject: Re: [Freesurfer] recon-all error: Correcting defect
External Email - Use CautionHello 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 (< fischl@nmr.mgh.harvard.edumailto:fischl@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 CautionI 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.edumailto: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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Diamond, Bram Ryder -
Miguel Ángel Rivas Fernández