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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



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