External Email - Use Caution
Hi there,
I am using Freesurfer v7.1.0 and encounter an error for few of my subjects only. Recon-all finishes with errors, and it seems this occurs during the segmentation.
What can I do to fix this?
I attached the recon-all log for one of my subject.
Thanks,
Yann
Can you upload the subject so I can take a look? Instructions below
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 6/15/2020 8:28 PM, Yann Quidé wrote:
External Email - Use Caution
Hi there,
I am using Freesurfer v7.1.0 and encounter an error for few of my subjects only. Recon-all finishes with errors, and it seems this occurs during the segmentation.
What can I do to fix this?
I attached the recon-all log for one of my subject.
Thanks,
Yann
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Doug,
Thanks for this. I sent the file; it’s called yannquide.tar.gz.
Yann
On 16 Jun 2020, at 11:56 pm, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Can you upload the subject so I can take a look? Instructions below
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu http://surfer.nmr.mgh.harvard.edu/ It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 6/15/2020 8:28 PM, Yann Quidé wrote:
External Email - Use CautionHi there,
I am using Freesurfer v7.1.0 and encounter an error for few of my subjects only. Recon-all finishes with errors, and it seems this occurs during the segmentation.
What can I do to fix this?
I attached the recon-all log for one of my subject.
Thanks,
Yann
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
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
External Email - Use Caution
Hi team,
I was just wondering if you received my file and if you had time to look at it?
Thanks,
Yann
On 18 Jun 2020, at 7:08 am, Yann Quidé yannquide@gmail.com wrote:
Hi Doug,
Thanks for this. I sent the file; it’s called yannquide.tar.gz.
Yann
On 16 Jun 2020, at 11:56 pm, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
Can you upload the subject so I can take a look? Instructions below
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu http://surfer.nmr.mgh.harvard.edu/ It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 6/15/2020 8:28 PM, Yann Quidé wrote:
External Email - Use CautionHi there,
I am using Freesurfer v7.1.0 and encounter an error for few of my subjects only. Recon-all finishes with errors, and it seems this occurs during the segmentation.
What can I do to fix this?
I attached the recon-all log for one of my subject.
Thanks,
Yann
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
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
External Email - Use Caution
Hi team,
I appreciate everyone is busy, but did anyone have time to look at my subject? It was uploaded on June 18. It’s called yannquide.tar.gz
Thanks for your time.
Yann
On 22 Jun 2020, at 12:51 pm, Yann Quidé yannquide@gmail.com wrote:
Hi team,
I was just wondering if you received my file and if you had time to look at it?
Thanks,
Yann
On 18 Jun 2020, at 7:08 am, Yann Quidé <yannquide@gmail.com mailto:yannquide@gmail.com> wrote:
Hi Doug,
Thanks for this. I sent the file; it’s called yannquide.tar.gz.
Yann
On 16 Jun 2020, at 11:56 pm, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
Can you upload the subject so I can take a look? Instructions below
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu http://surfer.nmr.mgh.harvard.edu/ It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 6/15/2020 8:28 PM, Yann Quidé wrote:
External Email - Use CautionHi there,
I am using Freesurfer v7.1.0 and encounter an error for few of my subjects only. Recon-all finishes with errors, and it seems this occurs during the segmentation.
What can I do to fix this?
I attached the recon-all log for one of my subject.
Thanks,
Yann
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
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
Hi Yann (and anyone else with mri_cc failures on mac), We have a fix that we'll include in an upcoming 7.1.1 patch release. If you'd like a quick local fix, you can update your distribution with the new version of mri_cc by running the following commands (this might require sudo): cd $FREESURFER_HOME/bin rm mri_cc curl https://surfer.nmr.mgh.harvard.edu/pub/dist/tmp_patch/mri_cc -O mri_cc chmod +x mri_cc Please let us know if this does not solve your issue. Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yann Quidé yannquide@gmail.com Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Monday, June 29, 2020 at 2:35 AM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error recon-all mri_cc
External Email - Use Caution Hi team,
I appreciate everyone is busy, but did anyone have time to look at my subject? It was uploaded on June 18. It’s called yannquide.tar.gz
Thanks for your time.
Yann
On 22 Jun 2020, at 12:51 pm, Yann Quidé <yannquide@gmail.commailto:yannquide@gmail.com> wrote:
Hi team,
I was just wondering if you received my file and if you had time to look at it?
Thanks,
Yann
On 18 Jun 2020, at 7:08 am, Yann Quidé <yannquide@gmail.commailto:yannquide@gmail.com> wrote:
Hi Doug,
Thanks for this. I sent the file; it’s called yannquide.tar.gz.
Yann
On 16 Jun 2020, at 11:56 pm, Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote:
Can you upload the subject so I can take a look? Instructions below
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.eduhttp://surfer.nmr.mgh.harvard.edu/ It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 6/15/2020 8:28 PM, Yann Quidé wrote: External Email - Use Caution
Hi there,
I am using Freesurfer v7.1.0 and encounter an error for few of my subjects only. Recon-all finishes with errors, and it seems this occurs during the segmentation.
What can I do to fix this?
I attached the recon-all log for one of my subject.
Thanks,
Yann _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Andrew,
Thanks for this. Just a quick follow up question: does that mean I will have to recon all all the other scans that did not show this error with v7.1.1 for consistency, or will it be fine to keep them processed with v7.1.0?
Thanks,
Yann
On 30 Jun 2020, at 2:04 am, Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:
Hi Yann (and anyone else with mri_cc failures on mac), We have a fix that we'll include in an upcoming 7.1.1 patch release. If you'd like a quick local fix, you can update your distribution with the new version of mri_cc by running the following commands (this might require sudo): cd $FREESURFER_HOME/bin rm mri_cc curl https://surfer.nmr.mgh.harvard.edu/pub/dist/tmp_patch/mri_cc https://surfer.nmr.mgh.harvard.edu/pub/dist/tmp_patch/mri_cc -O mri_cc chmod +x mri_cc Please let us know if this does not solve your issue. Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yann Quidé <yannquide@gmail.com mailto:yannquide@gmail.com> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, June 29, 2020 at 2:35 AM To: FS Help <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error recon-all mri_cc
External Email - Use CautionHi team,
I appreciate everyone is busy, but did anyone have time to look at my subject? It was uploaded on June 18. It’s called yannquide.tar.gz
Thanks for your time.
Yann
On 22 Jun 2020, at 12:51 pm, Yann Quidé <yannquide@gmail.com mailto:yannquide@gmail.com> wrote:
Hi team,
I was just wondering if you received my file and if you had time to look at it?
Thanks,
Yann
On 18 Jun 2020, at 7:08 am, Yann Quidé <yannquide@gmail.com mailto:yannquide@gmail.com> wrote:
Hi Doug,
Thanks for this. I sent the file; it’s called yannquide.tar.gz.
Yann
On 16 Jun 2020, at 11:56 pm, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
Can you upload the subject so I can take a look? Instructions below
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu http://surfer.nmr.mgh.harvard.edu/ It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 6/15/2020 8:28 PM, Yann Quidé wrote:
External Email - Use CautionHi there,
I am using Freesurfer v7.1.0 and encounter an error for few of my subjects only. Recon-all finishes with errors, and it seems this occurs during the segmentation.
What can I do to fix this?
I attached the recon-all log for one of my subject.
Thanks,
Yann
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
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
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
I think they should give the same result, but try one or two to confirm
On 6/29/2020 6:12 PM, Yann Quidé wrote:
External Email - Use Caution
Hi Andrew,
Thanks for this. Just a quick follow up question: does that mean I will have to recon all all the other scans that did not show this error with v7.1.1 for consistency, or will it be fine to keep them processed with v7.1.0?
Thanks,
Yann
On 30 Jun 2020, at 2:04 am, Hoopes, Andrew <AHOOPES@mgh.harvard.edu mailto:AHOOPES@mgh.harvard.edu> wrote:
Hi Yann (and anyone else with mri_cc failures on mac), We have a fix that we'll include in an upcoming 7.1.1 patch release. If you'd like a quick local fix, you can update your distribution with the new version of mri_cc by running the following commands (this might require sudo): cd $FREESURFER_HOME/bin rm mri_cc curlhttps://surfer.nmr.mgh.harvard.edu/pub/dist/tmp_patch/mri_cc-O mri_cc chmod +x mri_cc Please let us know if this does not solve your issue. Andrew *From:*<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yann Quidé <yannquide@gmail.com mailto:yannquide@gmail.com> *Reply-To:*FS Help <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> *Date:*Monday, June 29, 2020 at 2:35 AM *To:*FS Help <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:*Re: [Freesurfer] Error recon-all mri_cc * External Email - Use Caution * Hi team, I appreciate everyone is busy, but did anyone have time to look at my subject? It was uploaded on June 18. It’s called yannquide.tar.gz Thanks for your time. Yann
On 22 Jun 2020, at 12:51 pm, Yann Quidé <yannquide@gmail.com mailto:yannquide@gmail.com> wrote: Hi team, I was just wondering if you received my file and if you had time to look at it? Thanks, Yann
On 18 Jun 2020, at 7:08 am, Yann Quidé <yannquide@gmail.com mailto:yannquide@gmail.com> wrote: Hi Doug, Thanks for this. I sent the file; it’s called yannquide.tar.gz. Yann
On 16 Jun 2020, at 11:56 pm, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote: Can you upload the subject so I can take a look? Instructions below
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftpsurfer.nmr.mgh.harvard.edu http://surfer.nmr.mgh.harvard.edu/ It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 6/15/2020 8:28 PM, Yann Quidé wrote:
External Email - Use Caution
Hi there,
I am using Freesurfer v7.1.0 and encounter an error for few of my subjects only. Recon-all finishes with errors, and it seems this occurs during the segmentation.
What can I do to fix this?
I attached the recon-all log for one of my subject.
Thanks,
Yann
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Hoopes, Andrew -
Yann Quidé