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