Can you attach recon-all.log?
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Jeffrey Spielberg
Sent: Wednesday, March 19, 2025 9:15 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error using -nonuintensitycor
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Hello,
I'm running Freesurfer 8.0.0 on a Rocky machine and run into an error when I use the -nonuintensitycor flag. The same image finels run perfectly fine without that flag, but with the flag I get this error:
#@# Intensity Normalization Tue Mar 18 15:22:23 EDT 2025
/s3l/fs_subjects/RAD_2100A/mri
mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz
using max gradient = 1.000
setting seed for random number genererator to 1234
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from nu.mgz...
error: mghRead(/s3l/fs_subjects/RAD_2100A/mri/nu.mgz, -1): could not open file^@
error: mri_normalize: could not open source file nu.mgz^@
Command exited with non-zero status 255
This looks to be a bug - any ideas for a workaround? Thanks!
--
Jeffrey M. Spielberg, Ph.D.
Associate Professor, Clinical Science
Department of Psychological and Brain Sciences
University of Delaware, Newark, DE 19716
Office: 344 Building X
Lab: Suite 302 Building X
Email: jmsp@udel.edu
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