We fixed ‘-nonuintensitycor’ as you suggested – adding an else clause to
if($DoNuIntensityCor), recon-all line 2107.
if($DoNuIntensityCor) then
…
else
# link nu.mgz to orig.mgz
pushd $subjdir/mri
rm -f nu.mgz
ln -sf orig.mgz nu.mgz
popd
endif
From: Jeffrey Spielberg <j...@udel.edu>
Sent: Tuesday, April 1, 2025 2:07 PM
To: Huang, Yujing <yhuan...@mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: Error using -nonuintensitycor
External Email - Use Caution
I'm confused: -nonuintensitycor is listed as an option in the recon-all help,
and recon-all does accept it as an argument (i.e., on line 6575 of recon-all,
which is relevant for line 2050 and after). So it seems to me that there must
be a bug in 1 of two places: Either recon-all should be able to run with
-nonuintensitycor (but there is a bug in that process) OR -nonuintensitycor
should be removed from the recon-all help and recon-all shouldn't accept it as
an argument. Which of these is the case? If it's the first one, would the
workaround be to add an elif and then copy orig.mgz to nu.mgz? If it's the
second case, can you tell me the reason why this functionality has been removed?
As a little bit of context, parts of OFC/frontal pole are being consistently
excluded from the pial surface and we have found methods for inhomogeneity
correction that work better than ANTS N4. Thus, we have tried applying that
correction before inputting the T1 into freesurfer, which helps, but does not
fully fix the problem. One possibility is that the double correction (i.e.,
what we do beforehand and what is done in freesurfer) is undoing some of the
benefit of our initial correction, and thus we want to test this by bypassing
the freesurfer correction. However, as mentioned, this throws an error.
On Tue, Apr 1, 2025 at 11:38 AM Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> wrote:
I’m afraid that recon-all can’t be run with ‘-nonuintensitycor’ specified.
From: Jeffrey Spielberg <j...@udel.edu<mailto:j...@udel.edu>>
Sent: Tuesday, April 1, 2025 9:41 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>;
Huang, Yujing <yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Subject: Re: Error using -nonuintensitycor
External Email - Use Caution
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>
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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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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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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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