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

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 <jmsp@udel.edumailto:jmsp@udel.edu> wrote: Yup - here you go

On Wed, Mar 19, 2025 at 9:14 AM Jeffrey Spielberg <jmsp@udel.edumailto: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.edumailto:jmsp@udel.edu Web: http://sites.udel.edu/jmsp/ http://secure-web.cisco.com/146nhbaHT2u2FrKGAJsd-dbuBUXVIQMYkVxykBV1v9AlEQKMj_lhKtzajKC5fh5bTuXzduyT_8f6iK9memwUkUW40PKsTV4b4LPhx6WesWVx7tpN3SJxG8fR4nslkfXhIVBtMUylbgRbk-PPAoFgdCs-l5WnD3nlxWu8p_VV2j1HlRRtZCMBaMcvjfsEn0BZuoKpvruFqw033fyI77JfzBQUM5XuShIAUKzQCtAmjAxWTYM-GRfR8uEih7iZja58U6cnn_IVUYCdaGHE8ZsT-si2dxq4Fkgz5l6PprPpdu2HDMS0P0eNgkUjt7310JDXj/http%3A%2F%2Fsites.udel.edu%2Fjmsp%2F Personal Zoom: https://udel.zoom.us/j/9704489599https://secure-web.cisco.com/1if_GOD6b54WwxpyTat9Jp4Uv0EehfEqTNNAG76mcbnq9sWhy7mH1laE4nStIgGvGkrHqki-GeNDo0UINQXiFRQBst7Vw-ZrByEX08TUZZRPBSV5TLf72BW-AuAywcBmC55RI1BFCKi_hlg8-1_HjQjBmTXoqeB0mP51dQ5Qgm4AaHTAlqBbYZIhP94jKQ5LUs_1xdJd7wYWUEwIbSpS8ZidYPFH7Ytd5uGg-mWVuxprOFUJ7-gOyRrLyGzAxOKqKoRv7Ers13JFF0MYI3ukxKrElyEIpdunD3I2QgLidJK7jmCtPkODjX_9qFlhPxDNH/https%3A%2F%2Fudel.zoom.us%2Fj%2F9704489599

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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.edumailto:jmsp@udel.edu Web: http://sites.udel.edu/jmsp/ http://secure-web.cisco.com/146nhbaHT2u2FrKGAJsd-dbuBUXVIQMYkVxykBV1v9AlEQKMj_lhKtzajKC5fh5bTuXzduyT_8f6iK9memwUkUW40PKsTV4b4LPhx6WesWVx7tpN3SJxG8fR4nslkfXhIVBtMUylbgRbk-PPAoFgdCs-l5WnD3nlxWu8p_VV2j1HlRRtZCMBaMcvjfsEn0BZuoKpvruFqw033fyI77JfzBQUM5XuShIAUKzQCtAmjAxWTYM-GRfR8uEih7iZja58U6cnn_IVUYCdaGHE8ZsT-si2dxq4Fkgz5l6PprPpdu2HDMS0P0eNgkUjt7310JDXj/http%3A%2F%2Fsites.udel.edu%2Fjmsp%2F Personal Zoom: https://udel.zoom.us/j/9704489599https://secure-web.cisco.com/1if_GOD6b54WwxpyTat9Jp4Uv0EehfEqTNNAG76mcbnq9sWhy7mH1laE4nStIgGvGkrHqki-GeNDo0UINQXiFRQBst7Vw-ZrByEX08TUZZRPBSV5TLf72BW-AuAywcBmC55RI1BFCKi_hlg8-1_HjQjBmTXoqeB0mP51dQ5Qgm4AaHTAlqBbYZIhP94jKQ5LUs_1xdJd7wYWUEwIbSpS8ZidYPFH7Ytd5uGg-mWVuxprOFUJ7-gOyRrLyGzAxOKqKoRv7Ers13JFF0MYI3ukxKrElyEIpdunD3I2QgLidJK7jmCtPkODjX_9qFlhPxDNH/https%3A%2F%2Fudel.zoom.us%2Fj%2F9704489599

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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.edumailto:jmsp@udel.edu Web: http://sites.udel.edu/jmsp/ http://secure-web.cisco.com/146nhbaHT2u2FrKGAJsd-dbuBUXVIQMYkVxykBV1v9AlEQKMj_lhKtzajKC5fh5bTuXzduyT_8f6iK9memwUkUW40PKsTV4b4LPhx6WesWVx7tpN3SJxG8fR4nslkfXhIVBtMUylbgRbk-PPAoFgdCs-l5WnD3nlxWu8p_VV2j1HlRRtZCMBaMcvjfsEn0BZuoKpvruFqw033fyI77JfzBQUM5XuShIAUKzQCtAmjAxWTYM-GRfR8uEih7iZja58U6cnn_IVUYCdaGHE8ZsT-si2dxq4Fkgz5l6PprPpdu2HDMS0P0eNgkUjt7310JDXj/http%3A%2F%2Fsites.udel.edu%2Fjmsp%2F Personal Zoom: https://udel.zoom.us/j/9704489599https://secure-web.cisco.com/1if_GOD6b54WwxpyTat9Jp4Uv0EehfEqTNNAG76mcbnq9sWhy7mH1laE4nStIgGvGkrHqki-GeNDo0UINQXiFRQBst7Vw-ZrByEX08TUZZRPBSV5TLf72BW-AuAywcBmC55RI1BFCKi_hlg8-1_HjQjBmTXoqeB0mP51dQ5Qgm4AaHTAlqBbYZIhP94jKQ5LUs_1xdJd7wYWUEwIbSpS8ZidYPFH7Ytd5uGg-mWVuxprOFUJ7-gOyRrLyGzAxOKqKoRv7Ers13JFF0MYI3ukxKrElyEIpdunD3I2QgLidJK7jmCtPkODjX_9qFlhPxDNH/https%3A%2F%2Fudel.zoom.us%2Fj%2F9704489599

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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 jmsp@udel.edu Sent: Tuesday, April 1, 2025 2:07 PM To: Huang, Yujing YHUANG43@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 <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: I’m afraid that recon-all can’t be run with ‘-nonuintensitycor’ specified.

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

On Wed, Mar 19, 2025 at 9:14 AM Jeffrey Spielberg <jmsp@udel.edumailto: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.edumailto:jmsp@udel.edu Web: http://sites.udel.edu/jmsp/ http://secure-web.cisco.com/146nhbaHT2u2FrKGAJsd-dbuBUXVIQMYkVxykBV1v9AlEQKMj_lhKtzajKC5fh5bTuXzduyT_8f6iK9memwUkUW40PKsTV4b4LPhx6WesWVx7tpN3SJxG8fR4nslkfXhIVBtMUylbgRbk-PPAoFgdCs-l5WnD3nlxWu8p_VV2j1HlRRtZCMBaMcvjfsEn0BZuoKpvruFqw033fyI77JfzBQUM5XuShIAUKzQCtAmjAxWTYM-GRfR8uEih7iZja58U6cnn_IVUYCdaGHE8ZsT-si2dxq4Fkgz5l6PprPpdu2HDMS0P0eNgkUjt7310JDXj/http%3A%2F%2Fsites.udel.edu%2Fjmsp%2F Personal Zoom: https://udel.zoom.us/j/9704489599https://secure-web.cisco.com/1if_GOD6b54WwxpyTat9Jp4Uv0EehfEqTNNAG76mcbnq9sWhy7mH1laE4nStIgGvGkrHqki-GeNDo0UINQXiFRQBst7Vw-ZrByEX08TUZZRPBSV5TLf72BW-AuAywcBmC55RI1BFCKi_hlg8-1_HjQjBmTXoqeB0mP51dQ5Qgm4AaHTAlqBbYZIhP94jKQ5LUs_1xdJd7wYWUEwIbSpS8ZidYPFH7Ytd5uGg-mWVuxprOFUJ7-gOyRrLyGzAxOKqKoRv7Ers13JFF0MYI3ukxKrElyEIpdunD3I2QgLidJK7jmCtPkODjX_9qFlhPxDNH/https%3A%2F%2Fudel.zoom.us%2Fj%2F9704489599

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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.edumailto:jmsp@udel.edu Web: http://sites.udel.edu/jmsp/ http://secure-web.cisco.com/146nhbaHT2u2FrKGAJsd-dbuBUXVIQMYkVxykBV1v9AlEQKMj_lhKtzajKC5fh5bTuXzduyT_8f6iK9memwUkUW40PKsTV4b4LPhx6WesWVx7tpN3SJxG8fR4nslkfXhIVBtMUylbgRbk-PPAoFgdCs-l5WnD3nlxWu8p_VV2j1HlRRtZCMBaMcvjfsEn0BZuoKpvruFqw033fyI77JfzBQUM5XuShIAUKzQCtAmjAxWTYM-GRfR8uEih7iZja58U6cnn_IVUYCdaGHE8ZsT-si2dxq4Fkgz5l6PprPpdu2HDMS0P0eNgkUjt7310JDXj/http%3A%2F%2Fsites.udel.edu%2Fjmsp%2F Personal Zoom: https://udel.zoom.us/j/9704489599https://secure-web.cisco.com/1if_GOD6b54WwxpyTat9Jp4Uv0EehfEqTNNAG76mcbnq9sWhy7mH1laE4nStIgGvGkrHqki-GeNDo0UINQXiFRQBst7Vw-ZrByEX08TUZZRPBSV5TLf72BW-AuAywcBmC55RI1BFCKi_hlg8-1_HjQjBmTXoqeB0mP51dQ5Qgm4AaHTAlqBbYZIhP94jKQ5LUs_1xdJd7wYWUEwIbSpS8ZidYPFH7Ytd5uGg-mWVuxprOFUJ7-gOyRrLyGzAxOKqKoRv7Ers13JFF0MYI3ukxKrElyEIpdunD3I2QgLidJK7jmCtPkODjX_9qFlhPxDNH/https%3A%2F%2Fudel.zoom.us%2Fj%2F9704489599

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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

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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

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