Freesurfer February 2023

freesurfer@nmr.mgh.harvard.edu

85 participants
122 discussions

Senior research position
by Aaron Tanenbaum 06 Feb '23

06 Feb '23

External Email - Use Caution Please see attached for a Senior research position job description. Please apply for the position at https://secure-web.cisco.com/1u02-AJuClQt7sTxQ63p9YV9P4EzHp2M0YbFhpmhtEnqyD… Do not apply for the position over email, email will be ignored. Aaron Tanenbaum

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Re: [Freesurfer] FS FAST
by fsbuild 06 Feb '23

06 Feb '23

External Email - Use Caution Hello Justin, Depending upon the OS of the machine, there may not be a “python” installed by default on the system, i.e., you need to choose either python2 or python3.  Given some scripts may still look for “python”, then you can add an alias in your shell init file so “python” points to what’s available. - R. ubuntu20:~$ which python ubuntu20:~$ which python2 ubuntu20:~$ which python3 /bin/python3ubuntu20:~$ python3 --version Python 3.8.10 ubuntu20:~$ alias python='python3' ubuntu20:~$ python --version Python 3.8.10 On Feb 6, 2023, at 00:53, Justin Oh <ohjp89(a)gmail.com> wrote:        External Email - Use Caution        Hi all, I am trying to run preproc-sess on a resting state MRI. I believe my directory is set the way it should be. There was an error that stopped the pipeline: env: python: No such file or directoryCould anybody help me out? All the best,Justin Oh_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FS FAST
by Justin Oh 06 Feb '23

06 Feb '23

External Email - Use Caution Hi all, I am trying to run preproc-sess on a resting state MRI. I believe my directory is set the way it should be. There was an error that stopped the pipeline: env: python: No such file or directory Could anybody help me out? All the best, Justin Oh

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TRACULA cluster statistics visualization
by miracle ozzoude 04 Feb '23

04 Feb '23

External Email - Use Caution I have a similar question to this unanswer one (see link) https://secure-web.cisco.com/1TPpYYjX_nTrm6lqczxoG15eSKbWRPZCXEekOMWT-xtyur… *Also* 1) If I run along-tract stats with mri_glmfit/mri_glmfit-sim and I found a significant result, how do I know the entire length of the tract and how much was affected? Also, is it measured in mm? 2) When performing clusterwise correction for multiple comparison for along-tract analyses, should the bonferroni flag (--2spaces) be included? This is because it wasn't mentioned/included in the tracula statistics tutorial nor the publication "Using diffusion MRI data acquired with ultra-high gradient strength to improve tractography in routine-quality data ". Many thanks, Paul

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Re: [Freesurfer] installation of two versions of freesurfer on same computer...
by fsbuild 03 Feb '23

03 Feb '23

External Email - Use Caution It should work to use multiple versions on the same machine.  You need to: (1) install them under different paths; (2) have enough disk space for each distribution; (3) change the setting of FREESURFER_HOME when you change the freesurfer version in use.   Then you need to re-source the SetUpFreeSurfer.[sh,csh] script each time you change FREESURFER_HOME to (re)set the shell environment. The package installers, *.rpm, *.deb, *.pkg, will install under a known path, i.e.., linux is /usr/local/freesurfer/<version> and for MacOS /Applications/freesurcer/<version>. The package management software on linux OS’s keeps track of the version that’s installed.  I think if you had  /usr/local/freesurfer/7.3.1 installed, then it would consider installing 7.3.2 as an upgrade to 7.3.1, and so it might remove 7.3.1 before installing 7.3.2 as  /usr/local/freesurfer/7.3.2.   There might be an option to tell the package tools to say to keep an old version.  You could make a copy of 7.3.1, install the 7.3.2 package, and then restore 7.3.1 so you have /usr/local/freesurfer/{7.3.1,7.3.2}.  I would try to have at least 1 version installed on Linux using the .deb or .rpm package installers.  That will have checked your machine and potentially installed dependencies fressurfer needs to run.  You could subsequently try using the tar archive for a different version located elsewhere, expanded as a non-root user. - R. On Feb 3, 2023, at 17:26, Gonzalo Rojas Costa <gonzalo.rojas.costa(a)gmail.com> wrote:        External Email - Use Caution        Hi:  How can I install two different versions of freesurfer on the same computer?  Sincerely,Gonzalo Rojas Costa_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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installation of two versions of freesurfer on same computer...
by Gonzalo Rojas Costa 03 Feb '23

03 Feb '23

External Email - Use Caution Hi: How can I install two different versions of freesurfer on the same computer? Sincerely, Gonzalo Rojas Costa

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Ubuntu compatibility
by Rachel Wagner 03 Feb '23

03 Feb '23

External Email - Use Caution Hello, I am trying to use mri_easyreg on Ubuntu 18 and realize I need to upgrade to freesurfer 7.3.2 to use this function. I am encountering issues downloading 7.3.2. Are the two compatible? Is there a link for setup I should follow? Thanks, Rachel

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Directory not set properly?
by Rachel Wagner 03 Feb '23

03 Feb '23

External Email - Use Caution Hello, I am trying to run recon-all on my data and am encountering the following issue: developer@developer-VirtualBox:~/freesurfer$ recon-all -subject 3T00300 -i /usr/home/developer/desktop/TIWI.nii -T2 /usr/home/developer/desktop/T2_Flair.nii -T2pial -all ERROR: cannot find /usr/home/developer/desktop/TIWI.nii Linux developer-VirtualBox 5.4.0-137-generic #154~18.04.1-Ubuntu SMP Tue Jan 10 16:58:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 3T00300 exited with ERRORS at Fri Feb 3 10:49:02 EST 2023 For more details, see the log file To report a problem, see http://secure-web.cisco.com/1bRGI0GFgxZrKH_-NM5aKbo8jy3AYVqO8EQuizksRFT_koq… developer@developer-VirtualBox:~/freesurfer$ recon-all -subject 3T00300 -i sample-001.mgz ERROR: cannot find sample-001.mgz Linux developer-VirtualBox 5.4.0-137-generic #154~18.04.1-Ubuntu SMP Tue Jan 10 16:58:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 3T00300 exited with ERRORS at Fri Feb 3 10:52:53 EST 2023 For more details, see the log file To report a problem, see http://secure-web.cisco.com/1bRGI0GFgxZrKH_-NM5aKbo8jy3AYVqO8EQuizksRFT_koq… developer@developer-VirtualBox:~/freesurfer$ Is it that my path is not set correctly? Thank you! Rachel Wagner

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Error:mghRead
by Lauren Stephens 03 Feb '23

03 Feb '23

External Email - Use Caution Hi Freesurfer Developers, I am attempting to open a NIFTI file in freeview. Freeview will open however, it gives the error "Failed to load MRI" and then the location and name of the file. We did verify that the nifti file does open regularly when accessed on the desktop. Below is the code used and the error in the terminal. What suggestions do you have to get the file to open in freeview? Last login: Tue Jan 31 13:34:25 on ttys001 -bash: $: command not found -------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/7.1.1 FSFAST_HOME /Applications/freesurfer/7.1.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.1.1/subjects MNI_DIR /Applications/freesurfer/7.1.1/mni FSL_DIR /usr/local/fsl PSYC-C02DP05D0833:~ corpuscallosum$ cd Desktop/freesurfer_qc PSYC-C02DP05D0833:freesurfer_qc corpuscallosum$ freeview -v \ > CS040/mri/brainmask.mgz \ > CS040/mri/wm.mgz:visible=0 \ > CS040/mri/orig.mgz:visible=0 \ > CS040/mri/aparc.a2009s+aseg.mgz:visible=0 \ > -f CS040/surf/lh.white:edgecolor=yellow \ > CS040/surf/rh.white:edgecolor=yellow \ > CS040/surf/rh.pial:edgecolor=red \ > CS040/surf/lh.pial:edgecolor=red \ > -viewport cor -layout 4 error: mghRead(/Users/corpuscallosum/Desktop/freesurfer_qc/CS040/mri/brainmask.mgz, -1): could not open file MRIread failed: Unable to read from /Users/corpuscallosum/Desktop/freesurfer_qc/CS040/mri/brainmask.mgz PSYC-C02DP05D0833:freesurfer_qc corpuscallosum$ We are using a Mac on Ventura 13.2, Terminal Version 2.13. Freesurfer version 7.1.1. Thank you, Lauren Stephens Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

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T2pial: Numerical argument out of domain
by AmirHussein Abdolalizadeh 03 Feb '23

03 Feb '23

External Email - Use Caution Hi Freesurfer enthusiasts/experts, I am running recon-all on the T1 sample of Parkinson's disease patients (with addition of T2) and it returns with this error, which I assume is due to T2pial: Creating pial distance volumes t=0.778738 (box.dx, box.dy, box.dz) = (146, 216, 328) (region->dx, region->dy, region->dz) = (146, 216, 328) (region->dx, region->dy, region->dz) = (146, 216, 328) locating cortical regions not in interior range [110.0 --> 300.0], and not in exterior range [130.0 --> 300.0] t = 1.39027 Starting loop over 125867 vertices vno = 0, t = 1.39027 error: Numerical argument out of domain error: MRIhistogramLabelRegion: constant image^@ error: Numerical argument out of domain error: MRIhistogramLabelRegion: constant image^@ The FreeSurfer version being used (in the head of the log file) is "freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275" Looking forward to your comments. Best, Amir

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Freesurfer February 2023