I’m afraid that recon-all can’t be run with ‘-nonuintensitycor’ specified.
From: Jeffrey Spielberg <j...@udel.edu>
Sent: Tuesday, April 1, 2025 9:41 AM
To: freesurfer@nmr.mgh.harvard.edu; Huang, Yujing <yhuan...@mgh.harvard.edu>
Subject: Re: Error using -nonuintensitycor
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Hi all - just wondering if any workaround had been identified for this error.
I'm reattaching the recon-all.log in case it's helpful
On Wed, Mar 19, 2025 at 9:51 AM Jeffrey Spielberg
<j...@udel.edu<mailto:j...@udel.edu>> wrote:
Yup - here you go
On Wed, Mar 19, 2025 at 9:14 AM Jeffrey Spielberg
<j...@udel.edu<mailto:j...@udel.edu>> wrote:
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: j...@udel.edu<mailto:j...@udel.edu>
Web: http://sites.udel.edu/jmsp/
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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: j...@udel.edu<mailto:j...@udel.edu>
Web: http://sites.udel.edu/jmsp/
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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: j...@udel.edu<mailto:j...@udel.edu>
Web: http://sites.udel.edu/jmsp/
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