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-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas
N. Greve" <dgr...@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.p...@emory.edu>
<mailto:james.kunwoo.p...@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
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