Freesurfer April 2025

freesurfer@nmr.mgh.harvard.edu

40 participants
53 discussions

Re: [Freesurfer] Search the archives link is not working
by fsbuild 08 Apr '25

08 Apr '25

External Email - Use Caution  I can reach this URL,https://secure-web.cisco.com/1he9MZver8hcuQJFs-vJQC4CflnTxZIHGyJzzULPJv… R. On Apr 8, 2025, at 16:44, Billah, Tashrif <tbillah(a)bwh.harvard.edu> wrote:Hi all, The "search the archives" link, found in FreeSurferSupport webpage, is not working:http://secure-web.cisco.com/1FOB0N8PjWPL99kzHL3Ba-5jNErWhFlNKUPmT8J… Is this expected? Best, Tashrif_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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nu_correct error: Can't locate Sys/Hostname.pm in @INC
by Billah, Tashrif 08 Apr '25

08 Apr '25

Hi all, In freesurfer-7.4.1, the nu_correct command gives this error: ``` Can't locate Sys/Hostname.pm in @INC (you may need to install the Sys::Hostname module) (@INC contains: /software/rocky9/freesurfer-7.4.1/mni/share/perl5 /usr/local/lib64/perl5/5.32 /usr/local/share/perl5/5.32 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5) at /software/rocky9/freesurfer-7.4.1/mni/share/perl5/MNI/MiscUtilities.pm line 36. BEGIN failed--compilation aborted at /software/rocky9/freesurfer-7.4.1/mni/share/perl5/MNI/MiscUtilities.pm line 36. Compilation failed in require at /software/rocky9/freesurfer-7.4.1/mni/share/perl5/MNI/Spawn.pm line 35. BEGIN failed--compilation aborted at /software/rocky9/freesurfer-7.4.1/mni/share/perl5/MNI/Spawn.pm line 35. Compilation failed in require at /software/rocky9/freesurfer-7.4.1/mni/bin/nu_correct line 38. BEGIN failed--compilation aborted at /software/rocky9/freesurfer-7.4.1/mni/bin/nu_correct line 3 ``` We are in Redhat 9 OS. Is this expected? Could you recommend a solution? Best, Tashrif

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Search the archives link is not working
by Billah, Tashrif 08 Apr '25

08 Apr '25

Hi all, The "search the archives" link, found in FreeSurferSupport webpage, is not working: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ Is this expected? Best, Tashrif

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FreeSurfer 8 on Ubuntu 24.04
by Nagesh Adluru 08 Apr '25

08 Apr '25

External Email - Use Caution Dear FreeSurfer development team, Could you kindly let us know if FreeSurfer 8 native installer for Ubuntu 24.04 would be released sometime in the near future? Thank you so much for the help and guidance. Please let us know if you have any questions or suggestions. Sincerely, Nagesh

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Error using -nonuintensitycor
by Jeffrey Spielberg 07 Apr '25

07 Apr '25

External Email - Use Caution 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(a)udel.edu Web: http://secure-web.cisco.com/1kOZT8vAxRUMrcZR3lkwUFNSIHUk1cRyGyu1QIlfYEHDpjV… Personal Zoom: https://secure-web.cisco.com/1PQ64OpYtuV98rydOWj5-yZN6p9Fy4OUwzLD2N9sfyBBF7… Please be aware that e-mail communication can be intercepted in transmission or misdirected. Please consider communicating any sensitive information by telephone, fax, or mail. The information contained in this message may be privileged and confidential. If you are NOT the intended recipient, please notify the sender immediately and destroy this message.

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cvs register error
by Xuesong Su 07 Apr '25

07 Apr '25

External Email - Use Caution Dear all, I am attempting to use my own data and follow the instructions on the petsurfer wiki. I ran the following command: `mri_cvs_register --mov 001 --template cvs_avg35_inMNI152` The output showed: [...] `mri_cvs_register: Step 1 (spherical registration) took 542 seconds` `surf2vol: Command not found.` It appears that Step 1 has been completed, but it's stuck on Step 2. So, I tried running: `mri_cvs_register --mov 001 --template cvs_avg35_inMNI152 --step2 --nocleanup` However, the output still returned `surf2vol: Command not found.` Prior to this, I had already set the `$SUBJECTS_DIR` environment variable and copied `/Applications/freesurfer/dev/subjects/cvs_avg35_inMNI152` to the `$SUBJECTS_DIR` directory. (1) Platform: MacBook Pro M2, macOS 15.3.2, (2) FreeSurfer version: freesurfer-macOS-darwin_arm64-dev-20240909-9ca95c6, downloaded from https://secure-web.cisco.com/13S72PTy2Rml5OEF_iEDV7rKCaavxBKyn_pl6E6oQ4EUXh… Thanks, XS

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license.txt
by Mohammed Hassan ALMorabet 07 Apr '25

07 Apr '25

External Email - Use Caution where the license.txt

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samseg: unrecognized flag with --lesion-mask-pattern
by Simone Cauzzo 07 Apr '25

07 Apr '25

External Email - Use Caution Dear support I'm running samseg using Freesurfer 7.4.0. I'm using t1, t2 and flair as input. I'm not sure if it's necessary to specify --lesion-mask-pattern but if I try, I get an unrecognized flag error as it reads the second input to --lesion-mask-pattern as a new flag. Log: ERROR: Flag 1 unrecognized. --t1w [...]/001.mgz --flair [...]/oFL.mgz --t2w [...]/oT2.mgz --s [...]01 --recon --use-flair --refmode t1w --pallidum-separate --lesion --fill --threads 16 --lesion-mask-pattern 0 1 1 if I remove the "--lesion-mask-pattern 0 1 1" I don't get any error. Any suggestion? Thanks Simone

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samseg: erroneous lesion labels on T2 red nucleus set to zero
by Simone Cauzzo 07 Apr '25

07 Apr '25

External Email - Use Caution Dear support I'm running the following command in Freesurfer 7.4: samseg --t1w ${SUBJECTS_DIR}/subjOPA${ss}/mri/orig/001.mgz --flair ${SUBJECTS_DIR}/subjOPA${ss}/mri/orig/oFL.mgz --t2w ${SUBJECTS_DIR}/subjOPA${ss}/mri/orig/oT2.mgz --s subjOPA${ss} --refmode t1w --pallidum-separate --lesion --fill --threads 16 --save-posteriors everything runs smoothly, but when I check the results I see some holes in the midbrain, in particular the red nucleus is labeled as csf. If I look at the T2.mgz file in the mri folder (I also run samseg2recon so I'm not sure it is the name given by samseg) I see that the red nucleus is set to zero, despite having non-zero values in the T2.norm.mgz volume. Two questions: 1) how can I avoid low-intensity T2 regions to be set to CSF? 2) is it possible to provide a brain mask to samseg if I already have a reliable one? [image: Screenshot from 2025-04-02 15-20-51.png] Simone Cauzzo

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Missing data for diffusion processing tutorial
by Andrei Bieger 06 Apr '25

06 Apr '25

External Email - Use Caution Dear Freesurfer developers, I am trying to follow the Diffusion Processing Tutorial (https://secure-web.cisco.com/1ck8X8dlcraSHUFUd5cZoLiUQsXCM6JLEEH7rZnRzPLrjF…) while using tutorial data from the Freesurfer Tutorial Datasets (https://secure-web.cisco.com/1Ju0TalvW2sEV8I-BJvXQvCMSvz6QCUYH9pTC2BWw9YWxy…) After preparing the environment variables and starting Freesurfer, the next step would be dt_recon --b bvals.dat bvecs.dat --i $TUTORIAL_DIR/$subj/orig/6-1.dcm --s $subj --o $TUTORIAL_DIR/$subj/dtrecon The problem is, there is no …/Diff001/orig in the tutorial data, only the dtrecon folder, as you can see below: Can you help me with this? Thank you in advance, Andrei

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Freesurfer April 2025