I’m afraid that recon-all can’t be run with ‘-nonuintensitycor’ specified.

 

From: Jeffrey Spielberg <jmsp@udel.edu>
Sent: Tuesday, April 1, 2025 9:41 AM
To: freesurfer@nmr.mgh.harvard.edu; Huang, Yujing <YHUANG43@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 <jmsp@udel.edu> wrote:

Yup - here you go

 

On Wed, Mar 19, 2025 at 9:14 AM Jeffrey Spielberg <jmsp@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:    jmsp@udel.edu

 

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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:    jmsp@udel.edu

 

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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:                                   jmsp@udel.edu

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