It looks like seg2recon is also looking for FREESURFER. Set it to your
Freesurfer install directory, same as FREESURFER_HOME.
From: Maya Yablonski
Sent: Tuesday, October 31, 2023 7:08 PM
To: Huang, Yujing
Subject: Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs
External Email - Use Caution
Hi Woo-Suk,
The change you suggested did work when i made a second attempt. The files were
getting mixed in with the trac-preproc copy I created in case of errors.
Thank you,
Lauren Stephens
Lauren Stephens, MS
Assistant Clinical Research Coordi
Can you try to set environment variable FS_ALLOW_DEEP before running 'recon-all
-synthseg'.
If you are using tcsh or csh, do 'setenv FS_ALLOW_DEEP 1'.
If you are using bash, do 'export FS_ALLOW_DEEP=1'.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Iglesias Gonzalez
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Hello,
I am working on a project using FreeSurfer, and I am trying to set up a
whole brain group analysis. However, I am not sure how to set up the FSDG
files, etc., as my dependent variable is not a cortical measurement. My
dependent variable is a neu
I’ll defer to the software engineers for the first issue!
For the second: does it work if you copy norm.mgz into orig/001.mgz? :-D
--
Juan Eugenio Iglesias
http://www.jeiglesias.com
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Maya Yablonski
Date: Tuesday, October 31, 2023 at 1:
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Hello,
Any help with this issue is greatly appreciated.
I am trying to import the Neuromorphometrics atlas into Freesurfer as a part of
my segmentation analysis. I have run recon-all on my template subject (IXI550)
and the subject to register (PSCI1
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Thanks! When I tried
"recon-all -synthseg -subjid sub-xx -i .nii.gz"
I get an error that only says: ERROR: cannot use ML routines
The same happened on an HPC cluster (linux) and on my local mac. I tried both
Freesurfer 7.3.2 and 7.4.1.
I have no issues
