Freesurfer January 2024

freesurfer@nmr.mgh.harvard.edu

70 participants
111 discussions

Freeview crashes when trying to load volumes
by Ford, Jamie K 12 Jan '24

12 Jan '24

External Email - Use Caution Hello, Please could I get some advice on my installation? I've downloaded version 7.4.0 using the same steps described in the installation video https://secure-web.cisco.com/1f3eoE6wiYWgcSSn4HiWKsg1DLQo_L2RuFn8xDGE0ZoFRi… Everything seems fine until I try to load any sort of volume, e.g., a Bert MRI file (like on the video). Freeview then crashes. This is the same for any volume. Could someone please advice? Any guidance would be greatly appreciated. Many Thanks, Jamie

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Longitudinal TRACULA Thalamic segmentation failure
by Brendan Angelo 11 Jan '24

11 Jan '24

External Email - Use Caution Hi experts, I have been attempting to analyze a group of subjects through the longitudinal TRACULA pipeline and have run into many issues regarding the preprocessing step making use of the thalamic segmentation. I've combed through the archives on this topic and have found many different threads relating to issues with the necessary files for the thalamic segmentation not being created, particularly the aparc+aseg+thalnuc.nii.gz file during the trac-all -prep step. I am attempting these analyses on a newer Mac Studio computer and cannot make use of the MATLAB 2014b runtime to segment the thalamus with the old script. Using the suggestions from this<https://secure-web.cisco.com/1t4cK7l09VEg6fqBR20KopNrVyhT0Q4mm45aUdJMiOcUDS…> previous question, I ran the segment_subregions thalamus python script and renamed all the outputs to match the MATLAB outputs (ThalamicNuclei.v12.T1.FSvoxelSpace.mgz, ThalamicNuclei.v12.T1.mgz, ThalamicNuclei.v12.T1.volumes.txt), but still ran into errors with the prep script and creation of the aparc+aseg+thalnuc.nii.gz file mentioned above. It seems like all the previous threads on this issue result in no permanent solution, are there any suggestions on ways to fix this, at least temporarily? Any discussion on this topic would be appreciated. I've also attached the log files from one of my failed runs, as well as the TRACULA configuration file. This was all done on Freesurfer 7.4.1. Thanks, Brendan Brendan Angelo, MS BRANCH Lab USC

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Trouble with ssh tunneling & Freeview
by Dong, Yilei 11 Jan '24

11 Jan '24

External Email - Use Caution Hi Freesurfer team, I have Freesurfer installed on UCSD's Expanse HPC, which uses the Rocky Linux 8 operating system. Whenever we try to do ssh tunneling and more specifically, logging into our HPC via ssh -X to open up Freeview's GUI, it always aborts. Prior to logging into my HPC from my Mac laptop's terminal, I always open up XQuartz. Another colleague of mine has also encountered similar issues, where they have managed to get X11 and Xeyes to run, but also Freeview's window keeps aborting. We have also tried to follow instructions from the following links when it comes to getting ssh tunneling to work correctly in hopes of making Freeview's GUI pop up: https://secure-web.cisco.com/1R4ZWuowqG86V3YyoRGTRpJOHdknCViNdSnswxzgoNUJh-… https://secure-web.cisco.com/1n_nrksVR91kPB04lGzr6COj_EYtJE9nZ9kVxcDWeDscsO… If we operate from a Mac computer, is it better to use a VNC or XQuartz for ssh tunneling? In addition, can we find an error log in Freesurfer's directory to find out exactly why Freeview keeps aborting in our circumstance? Thank you. Sincerely, Yilei

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Infant_recon_all generated surface does not align well with the provided aseg file
by Yanbin Niu 11 Jan '24

11 Jan '24

External Email - Use Caution Hi Freesurfers, I'm currently working on running infant_recon_all with our edited aseg.nii.gz for newborn data. However, we've encountered an issue where the generated surface does not align well with the provided aseg file. I have attached some screenshots as an example, in which a fold that infant_recon_all is failing to fully recognize. This problem seems consistent across the brain and subjects. I'm reaching out to inquire if anyone has experience with this issue and if there are specific parameters that we can adjust to address this issue. Here is the command we've been using: infant_recon_all --s sub-1041 --age 1 --inputfile ${SUBJECTS_DIR}/sub-1041/mprage.nii.gz --segfile ${SUBJECTS_DIR}/sub-1041/aseg.nii --masked ${SUBJECTS_DIR}/sub-1041/brain_mask.nii.gz Thank you, Yanbin Niu

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Use of infantFS and FS in the interval 2 - 4.5 years of age
by Michelangelo Fabbrizzi 11 Jan '24

11 Jan '24

External Email - Use Caution Dear FS experts, I see it is recommended to use infantFS below 2 years of age, whereas FS has been used for 4.5 years and above. I was wondering what could be used in the interval 2 - 4.5 years of age: which are benefits and drawbacks of both? Thanks, appreciated, Mic

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Inter-rater reliability
by Taylor, Lisa 10 Jan '24

10 Jan '24

External Email - Use Caution Hi there, Has anyone in this community used a form of inter-rater reliability measure for multiple people editing for one project? I have some PIs who are interested in doing this for a project where several labs will be editing Freesurfer for a project. I am a bit stumped as I have always just used visual review to ensure reliability/validity between editors. Also, would a inter-rater reliability measure be more effective than visual reviewing? Thank you for any insight you can provide! Lisa

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Re: [Freesurfer] Freeview keeps aborting.
by fsbuild 10 Jan '24

10 Jan '24

External Email - Use Caution  I would check with your IT support staff about the error including asking if the machines in your cluster are setup to display X Windows sessions with image viewing applications like Freeview.   If the machines support remote graphics, they should be able to tell you what you need to set in your terminal session for it to work.   But it could be they expect programs like freeview to run on your local client machine and read the image files/data over the network via NFS, etc. - R. On Jan 9, 2024, at 18:52, Dong, Yilei <yid025(a)health.ucsd.edu> wrote:        External Email - Use Caution        Dear freesurfer help, I have freesurfer installed on UCSD's Expanse HPC, which is on the Rocky Linux 8 operating system. Every time I try to open freeview, it always keeps aborting. How should I fix this so that freeview's GUI can be shown? I have included the screenshot for reference on the error. Thank you. Sincerely,Yilei <Screen Shot 2024-01-09 at 3.47.14 PM.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freeview keeps aborting.
by Dong, Yilei 09 Jan '24

09 Jan '24

External Email - Use Caution Dear freesurfer help, I have freesurfer installed on UCSD's Expanse HPC, which is on the Rocky Linux 8 operating system. Every time I try to open freeview, it always keeps aborting. How should I fix this so that freeview's GUI can be shown? I have included the screenshot for reference on the error. Thank you. Sincerely, Yilei

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Scratch Directory Permissions Denied
by Michael Ruvalcaba 09 Jan '24

09 Jan '24

External Email - Use Caution Hello, I am trying to run the recon -all function in my MATLAB pipeline using Freesurfer 6.0.0 and I have no issues with it. However, when I run the recon -all step using Freesurfer 7.2.0 and run the following command (the recon -all step finishes without error by the way): ft_read_mri([subdir '3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']); I get the following error: /bin/bash: /scratch/tp746feb5d_1e83_4141_b25d_1824a1cb209e.load_mgh.m.mgh: Permission denied The issue is there is no scratch file and it looks like between version 6.0.0 and 7.2.0 there is some extra lines of code that uses a scratch directory (which 6.0.0 doesn't) Does anyone have any input on this? I hope this made sense! Best, Michael Ruvalcaba

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[WARNING: ATTACHMENT UNSCANNED]FreeSurfer Error
by ERNEST KISSI 09 Jan '24

09 Jan '24

External Email - Use Caution Dear Freesurfer Developers, I am a graduate student working on Macromolecular Proton Fraction (MPF) and I need to generate parcellation for it using Freesurfer. I have read several articles that reported successful results with this method. However, I have encountered some errors when I tried to run Freesurfer on my data. Some of the errors are related to transformation at the talairach, and some are related to missing brain mask. I have been struggling with these issues for four days and I have not been able to process any of my data. I have an urgent deadline for my thesis presentation on Friday and I would appreciate your assistance. I have subscribed to the mailing list but I have not received a confirmation email yet. I have attached a screenshot of my registration and two examples of my T1 MPF images. Could you please test them on your end and let me know what the problem is and how to fix it? Thank you for your time and support. Sincerely,

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Freesurfer January 2024