Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all
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Sincerely, James Park
From: "Park, James" james.kunwoo.park@emory.edu Date: Tuesday, September 8, 2020 at 11:48 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all
Dear FreeSurfer Developers,
We have recently been exploring the recon -all option to analyze T1 MRI data and ran into an error specifically when utilizing the -parallel flag.
We specifically ran into errors at the cortical ribbon mask stage during the code we ran (shown below with some parts of the paths removed).
recon-all -i “…preOp_T1MRI_axial-anon.nii" -s "freesurfer_output" -sd “…/freesurfer_output" -all -parallel
When the same code was run without the -parallel flag, the recon-all line ran successfully.
This was run on a Mac with macOS Catalina Version 10.15.6 using FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.
The recon-all.log file has been attached here as a reference.
Thank you for your help in advance.
Sincerely, James Park Willie Lab, Dpt. of Neurosurgery, Emory
________________________________
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
The issue with the ribbon is something we recently became aware of. does it happen consistently for you? I can send you a recon-all that will fix this for you, just tell me which version you are running.
On 9/8/2020 11:49 AM, Park, James wrote:
External Email - Use Caution
Sincerely,
James Park
*From: *"Park, James" james.kunwoo.park@emory.edu *Date: *Tuesday, September 8, 2020 at 11:48 AM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all
Dear FreeSurfer Developers,
We have recently been exploring the recon -all option to analyze T1 MRI data and ran into an error specifically when utilizing the -parallel flag.
We specifically ran into errors at the cortical ribbon mask stage during the code we ran (shown below with some parts of the paths removed).
recon-all -i “…preOp_T1MRI_axial-anon.nii" -s "freesurfer_output" -sd “…/freesurfer_output" -all -parallel
When the same code was run without the -parallel flag, the recon-all line ran successfully.
This was run on a Mac with macOS Catalina Version 10.15.6 using FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.
The recon-all.log file has been attached here as a reference.
Thank you for your help in advance.
Sincerely,
James Park
Willie Lab, Dpt. of Neurosurgery, Emory
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hello,
Thank you for such a prompt response.
This has happened consistently and across multiple mac laptops that we utilize in our laboratory.
Below is the freesurfer version that we are utilizing as noted in the build-stamp.txt file: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
That would be great thank you so much.
Sincerely, James Park
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, September 8, 2020 at 12:06 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all
The issue with the ribbon is something we recently became aware of. does it happen consistently for you? I can send you a recon-all that will fix this for you, just tell me which version you are running.
On 9/8/2020 11:49 AM, Park, James wrote:
External Email - Use Caution
Sincerely, James Park
From: "Park, James" james.kunwoo.park@emory.edumailto:james.kunwoo.park@emory.edu Date: Tuesday, September 8, 2020 at 11:48 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all
Dear FreeSurfer Developers,
We have recently been exploring the recon -all option to analyze T1 MRI data and ran into an error specifically when utilizing the -parallel flag.
We specifically ran into errors at the cortical ribbon mask stage during the code we ran (shown below with some parts of the paths removed).
recon-all -i “…preOp_T1MRI_axial-anon.nii" -s "freesurfer_output" -sd “…/freesurfer_output" -all -parallel
When the same code was run without the -parallel flag, the recon-all line ran successfully.
This was run on a Mac with macOS Catalina Version 10.15.6 using FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.
The recon-all.log file has been attached here as a reference.
Thank you for your help in advance.
Sincerely, James Park Willie Lab, Dpt. of Neurosurgery, Emory
________________________________
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Try using this version of recon-all https://gate.nmr.mgh.harvard.edu/safelinks/greve/recon-all.711.parallel
On 9/8/2020 12:09 PM, Park, James wrote:
External Email - Use Caution
Hello,
Thank you for such a prompt response.
This has happened consistently and across multiple mac laptops that we utilize in our laboratory.
Below is the freesurfer version that we are utilizing as noted in the build-stamp.txt file:
freesurfer-darwin-macOS-7.1.1-20200811-8b40551
That would be great thank you so much.
Sincerely,
James Park
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Tuesday, September 8, 2020 at 12:06 PM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *[External] Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all
The issue with the ribbon is something we recently became aware of. does it happen consistently for you? I can send you a recon-all that will fix this for you, just tell me which version you are running.
On 9/8/2020 11:49 AM, Park, James wrote:
* External Email - Use Caution * Sincerely, James Park *From: *"Park, James" <james.kunwoo.park@emory.edu> <mailto:james.kunwoo.park@emory.edu> *Date: *Tuesday, September 8, 2020 at 11:48 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all Dear FreeSurfer Developers, We have recently been exploring the recon -all option to analyze T1 MRI data and ran into an error specifically when utilizing the -parallel flag. We specifically ran into errors at the cortical ribbon mask stage during the code we ran (shown below with some parts of the paths removed). recon-all -i “…preOp_T1MRI_axial-anon.nii" -s "freesurfer_output" -sd “…/freesurfer_output" -all -parallel When the same code was run without the -parallel flag, the recon-all line ran successfully. This was run on a Mac with macOS Catalina Version 10.15.6 using FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551. The recon-all.log file has been attached here as a reference. Thank you for your help in advance. Sincerely, James Park Willie Lab, Dpt. of Neurosurgery, Emory ------------------------------------------------------------------------ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). _______________________________________________ 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
External Email - Use Caution
Dear Freesurfer Team,
Thank you for this update.
How can I replace the current recon-all script with this new script? Do I just replace the recon-all script located in the “bin” folder with this new script?
Additionally, I was wondering if you knew when these changes might formally be incorporated in a later version of freesurfer.
Thank you again for your help in advance.
Sincerely, James Park
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, September 8, 2020 at 6:42 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all
Try using this version of recon-all https://gate.nmr.mgh.harvard.edu/safelinks/greve/recon-all.711.parallel
On 9/8/2020 12:09 PM, Park, James wrote:
External Email - Use Caution Hello,
Thank you for such a prompt response.
This has happened consistently and across multiple mac laptops that we utilize in our laboratory.
Below is the freesurfer version that we are utilizing as noted in the build-stamp.txt file: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
That would be great thank you so much.
Sincerely, James Park
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, September 8, 2020 at 12:06 PM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all
The issue with the ribbon is something we recently became aware of. does it happen consistently for you? I can send you a recon-all that will fix this for you, just tell me which version you are running.
On 9/8/2020 11:49 AM, Park, James wrote:
External Email - Use Caution
Sincerely, James Park
From: "Park, James" james.kunwoo.park@emory.edumailto:james.kunwoo.park@emory.edu Date: Tuesday, September 8, 2020 at 11:48 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all
Dear FreeSurfer Developers,
We have recently been exploring the recon -all option to analyze T1 MRI data and ran into an error specifically when utilizing the -parallel flag.
We specifically ran into errors at the cortical ribbon mask stage during the code we ran (shown below with some parts of the paths removed).
recon-all -i “…preOp_T1MRI_axial-anon.nii" -s "freesurfer_output" -sd “…/freesurfer_output" -all -parallel
When the same code was run without the -parallel flag, the recon-all line ran successfully.
This was run on a Mac with macOS Catalina Version 10.15.6 using FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.
The recon-all.log file has been attached here as a reference.
Thank you for your help in advance.
Sincerely, James Park Willie Lab, Dpt. of Neurosurgery, Emory
________________________________
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
_______________________________________________
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
On 9/9/2020 9:07 AM, Park, James wrote:
External Email - Use Caution
Dear Freesurfer Team,
Thank you for this update.
How can I replace the current recon-all script with this new script?
Do I just replace the recon-all script located in the “bin” folder with this new script?
Yes, but make a copy of the recon-all that is there already
Additionally, I was wondering if you knew when these changes might formally be incorporated in a later version of freesurfer.
Not sure, but we can probably release a patch fairly soon.
Thank you again for your help in advance.
Sincerely,
James Park
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Tuesday, September 8, 2020 at 6:42 PM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] [External] Re: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all
Try using this version of recon-all https://gate.nmr.mgh.harvard.edu/safelinks/greve/recon-all.711.parallel
On 9/8/2020 12:09 PM, Park, James wrote:
* External Email - Use Caution * Hello, Thank you for such a prompt response. This has happened consistently and across multiple mac laptops that we utilize in our laboratory. Below is the freesurfer version that we are utilizing as noted in the build-stamp.txt file: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 That would be great thank you so much. Sincerely, James Park *From: *<freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Tuesday, September 8, 2020 at 12:06 PM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *[External] Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all The issue with the ribbon is something we recently became aware of. does it happen consistently for you? I can send you a recon-all that will fix this for you, just tell me which version you are running. On 9/8/2020 11:49 AM, Park, James wrote: * External Email - Use Caution * Sincerely, James Park *From: *"Park, James" <james.kunwoo.park@emory.edu> <mailto:james.kunwoo.park@emory.edu> *Date: *Tuesday, September 8, 2020 at 11:48 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all Dear FreeSurfer Developers, We have recently been exploring the recon -all option to analyze T1 MRI data and ran into an error specifically when utilizing the -parallel flag. We specifically ran into errors at the cortical ribbon mask stage during the code we ran (shown below with some parts of the paths removed). recon-all -i “…preOp_T1MRI_axial-anon.nii" -s "freesurfer_output" -sd “…/freesurfer_output" -all -parallel When the same code was run without the -parallel flag, the recon-all line ran successfully. This was run on a Mac with macOS Catalina Version 10.15.6 using FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551. The recon-all.log file has been attached here as a reference. Thank you for your help in advance. Sincerely, James Park Willie Lab, Dpt. of Neurosurgery, Emory ------------------------------------------------------------------------ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). _______________________________________________ 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
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Douglas N. Greve -
Park, James