Freesurfer April 2023

freesurfer@nmr.mgh.harvard.edu

80 participants
105 discussions

Updating to Current Version of Freesurfer
by Lauren Stephens 05 Apr '23

05 Apr '23

External Email - Use Caution Hello, We have been using Freesurfer v7.1.1 to process our data. We want to update to the v7.3.2. Can we continue to use the files from v7.1.1 which have our edits applied on the 7.3.2 version? Do we need to re-run recon-all on the files now using the 7.3.2 version? Thank you.

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[FreeSurfer] error in talairach_afd
by Krystal Xiwing Yau 05 Apr '23

05 Apr '23

External Email - Use Caution Dear FreeSurfer experts, I am encountering the error below: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) As suggested, I have visited the website and followed these steps (https://secure-web.cisco.com/1sysqwtJ3yrcNBi951zfg6ki_eIkKSA8LC8npRZ7GbT_Bf…) However, I cannot move the bars as indicated; plus, there are no T1.mgz generated and the surf folder is empty. [cid:47451ebe-9ef9-4af4-8165-7a9c27bb0881] Much appreciated if anyone could advise. Thank you very much, Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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synthstrip error
by Salil Soman 05 Apr '23

05 Apr '23

External Email - Use Caution Hi, I am passing synthstrip an nii.gz file, and it keeps giving the error "ValueError: cannot determine file format from extension for test " (full error below). Any suggestions on how to fix this issue? The nifti files was made from dicom images using dcm2nnix. Thanks! Salil Configuring model on the CPU Running SynthStrip model version 1 Input image read from: test.nii.gz Traceback (most recent call last): File "/usr/local/freesurfer/7.3.2//python/scripts/mri_synthstrip", line 245, in <module> image.save(args.out) File "/usr/local/freesurfer/7.3.2/python/lib/python3.8/site-packages/surfa/core/framed.py", line 274, in save save_framed_array(self, filename, fmt=fmt) File "/usr/local/freesurfer/7.3.2/python/lib/python3.8/site-packages/surfa/io/framed.py", line 136, in save_framed_array raise ValueError(f'cannot determine file format from extension for {filename}') ValueError: cannot determine file format from extension for test

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How to use custom fill with up to other labels flag
by Dilara Erişen 05 Apr '23

05 Apr '23

External Email - Use Caution Hi, I want to create ROI labels by dividing the activation cluster from functional localizer scan into visual areas. I used to be able to do this by projecting the activation cluster together with visual area labels I have generated with retinotopy analysis onto the surface using tksurfer and using the flags: "up to functional values below threshold", "up to unlabeled" and "up to other labels". For example, if I want to fill the above threshold vertices in V2, it will fill it up to V1/V2 and V2/V3 boundaries. However, now that I moved my analysis pipeline to Freeview I'm having problems with "up to other labels" options. It prints "Did not fill/remove any vertices" on the terminal and nothing happens on the Freeview screen. Here are the steps I take: - I load the surface together with the overlay (functional localizer activation) and labels (from the retinotopy analysis: V1, V2 and V3) - I select the custom fill option and click on a vertex inside the visual area label. - I select "create new label" with "up to functional values below threshold", "up to unlabeled" and "up to other labels". - nothing happens (see attachment) Is this not the way the "up to other labels" option is intended to be used? If so, can you suggest another way to achieve my goal? Or is this a bug? Thank you, Dilara 1. FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76bhow 2. Platform: 22.04 LTS (Jammy Jellyfish) 3. uname -a: Linux ada 5.15.0-43-generic #46-Ubuntu SMP Tue Jul 12 10:30:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

2 1

FreeSurfer / Tracula segmentation between seed points?
by Christian Owen 05 Apr '23

05 Apr '23

External Email - Use Caution Hi, Does Freesurfer / Tracula provide any way to automatically segment a tract between two arbitrarily selected points? Christian

1 0

Re: [Freesurfer] Freeview segmentation fault
by fsbuild 04 Apr '23

04 Apr '23

External Email - Use Caution You can set the environment variable FS_LICENSE to point to your license file.  Some people set that in their shell init file, e.g., .bashrc, and keep the file license.txt in their home directory.  For example, $ cd $HOME$ head -1 license.txtme(a)somedomain.com        <—— email you used to register $ export FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEme(a)somedomain.com        <—— email you used to registerStarting with the Freesurfer 7.3.2 release, the Mac build used Xquartz 2.8.2.   If you are not already running 2.8.2 or newer then I would download and install the latest version of Xquartz from https://secure-web.cisco.com/1SXQ4X5w-vvi7X1Bgt8BsNVoSPV15hx0E9DH… - R.

1 0

Freeview segmentation fault
by OSE KADIRI 04 Apr '23

04 Apr '23

External Email - Use Caution Hello, I am having some trouble using Freeview on my university cluster with my MacBook (macOS Monterey version 12.4). Freeview works fine from a Windows machine, but when I try to view images (using XQuartz on my Mac), I get "segmentation fault." It does not seem to be a memory issue and I'm not using multiple screens. I can successfully run MATLAB and gnuplot using XQuartz. Any help is greatly appreciated! Thank you, Ose -- Ose Kadiri Staff Research Associate, Deters Lab Department of Integrative Biology & Physiology, UCLA Pronouns: she/her

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FLAIRpial bug
by Silvia De Francesco 04 Apr '23

04 Apr '23

External Email - Use Caution Dear developers, We encountered the bug related to the analysis with FLAIR in recon-all (recon-all -s ${subj} -i T1.nii.gz -FLAIR FLAIR.nii.gz -FLAIRpial -all). We obtain a worse segmentation with FLAIR than only with T1. We use FreeSurfer v. 7.3.2 We also tried to run the analysis placing the line PlaceMMPialSurf --mm_min_inside 50 --mm_max_inside 200 --mm_min_outside 10 --mm_max_outside 50 in the global-expert-options.txt file in the $SUBJECTS_DIR and run recon-all -s ${subj} -FLAIRpial -autorecon3, the output seems better but the pial is ever worst than with only T1. What does the values of mm_min_inside mm_max_inside mm_min_outside mm_max_outside mean? Some suggestions to solve this problem? Thank you Silvia

1 1

FreeSurfer VM pass code
by Toni Gurguí 04 Apr '23

04 Apr '23

External Email - Use Caution Hello, I would like to request the pass code for the FreeSurfer Virtual VM image. Best, T.

1 0

Volume extraction of thalamus subfields in v7.3.2
by Melissa Thalhammer 04 Apr '23

04 Apr '23

External Email - Use Caution Dear Freesurfers, as already mentioned in a mailing list post (https://secure-web.cisco.com/1SAqhNan43pmaxS84P-6UvHZVgMO0LlOO5VahC9RJjjs3L…) subfield_segmentation in FS v7.3.2 does not create a statsfile including the output volumes. Instead, some txt file is created in /mri (i.e., ThalamusNuclei.volumes.txt). For summarizing the volumes across subjects, neither asegstats2table (because it looks for *.stats files) nor the quantifyThalamicNuclei.sh is applicable to the new function subfield_segmentation output directly. I've just adapted quantifyThalamicNuclei.sh and changed line 55 to the new version txt file names (see attached). Best, Melissa

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Freesurfer April 2023