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.

 

James Park

 

Try using this version of recon-all
https://gate.nmr.mgh.harvard.edu/safelinks/greve/recon-all.711.parallel

        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>
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

 

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