Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

[FreeSurfer] SyntSR for noise reduction and/or cross-scanner comparisons
by Linnman, Clas,Ph.D. 01 Jun '23

01 Jun '23

External Email - Use Caution Hi FreeSurfers We are looking at cortical thickness after spinal cord injury in a pooled sample from three sites. All have 1x1x1 mm T1. Our current approach has been to exclude noisy data (16/159 participants), and to account for scanner differences using site as dummy variables. We are considering using SynthSR for two purposes: 1. reduce motion artefacts in (some) scans 2. better merge data between different scanner sites If using SynthSR for noise reduction seems like a good idea, is it best to then run SynthSR on ALL datasets for consistency? Best Clas Linnman

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Sourcing freesurfer
by Pedro henrique barradas 01 Jun '23

01 Jun '23

External Email - Use Caution Hello! I'm having a couple problems with the final installation steps When I attempt to export $FREESURFER_HOME=$HOME/freesurfer it tells me: * bash: export: ´#HOME/freesurfer=root/freesurfer`: not a valid identifier When I source it, it now says it cannot find the directory and gives back the following answers: * bash: /root/freesurfer/SetUpFreeSurfer.sh: No such file or directory I also tried doing "source SetUpFreeSurfer.sh" from the freesurfer directory and I got this response: * bash: /root/freesurfer/FreeSurferEnv.sh: No such file or directory Also, When I type echo $FREESURFER_HOME I get root/freesurfer But when I type pwd $FREESURFER_HOME it gives me c/mnt/Users/ASUS/Downloads/freesurfer I greatly appreciate any advice. Thank you Best wishes

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Re: [Freesurfer] Problem installing FreeSurfer
by fsbuild 01 Jun '23

01 Jun '23

External Email - Use Caution Please make sure you have downloaded a freesurfer license.txt file by filling out the form at,https://secure-web.cisco.com/1jgHYKP0gy8_587mR2rxpzl3o6QwcsGjVygS8rScUOs… Place the license.txt file you will receive in your home directory, e.g.,  $ cd $HOME$ head -1 license.txt<email you used to register> Set the FS_LICENSE environment variable manually (and/or in your shell initialization file, e.g., .bashrc) to point to the license file,… here set from a terminal window running bash shell ... $ export FS_LICENSE=$HOME/license.txt Setup the freesurfer environment, $ export FREESURFER_HOME=/Applications/freesurfer/7.4.0$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.4.0-20230504-55dcf98 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.4.0 FSFAST_HOME       /Applications/freesurfer/7.4.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.4.0/subjects MNI_DIR           /Applications/freesurfer/7.4.0/mni $ which freeview/Applications/freesurfer/7.4.0/bin/freeview Then try running freeview with no arguments to see if it brings up an empty window, $ freeview If that works, quit freeview and try running it again with an example volume included in the distribution, $ freeview  $SUBJECTS_DIR/bert/mri/brain.mgz If that works, quit freeview and try your own surface/volume files. - R. On May 31, 2023, at 17:05, Michelangelo Fabbrizzi <michefabb(a)gmail.com> wrote:        External Email - Use Caution        Dear Sirs,I am new to Freesurfer. I installed as shown on website and added the license.txt, however when I open freeview I get an error "/Applications/freesurfer/7.4.0/bin/freeview: riga 2:  2047 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“”Attached the report.Freesurfer version: freesurfer-darwin-macOS-7.4.0-20230510-e558e6ePlatform: MacOS12.6.6Mac: Macbook Pro Intel Core i5 dual-coreXQuartz2..8.15XQuartz2.8.5Can you help me please?Thanks!Michelangelo<report.txt>

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pass code
by Agosti, Giulia 01 Jun '23

01 Jun '23

External Email - Use Caution Hello, I am following the instruction from this page: freesurfer(a)nmr.mgh.harvard.edu and a pass code is needed for this 7z archieve. Could you send me the pass code? Kind regards

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Problem installing FreeSurfer
by Michelangelo Fabbrizzi 31 May '23

31 May '23

External Email - Use Caution Dear Sirs, I am new to Freesurfer. I installed as shown on website and added the license.txt, however when I open freeview I get an error "/Applications/freesurfer/7.4.0/bin/freeview: riga 2: 2047 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“” Attached the report. Freesurfer version: freesurfer-darwin-macOS-7.4.0-20230510-e558e6e Platform: MacOS12.6.6 Mac: Macbook Pro Intel Core i5 dual-core XQuartz2.8.15 XQuartz2.8.5 Can you help me please? Thanks! Michelangelo

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Re: [Freesurfer] source freesurfer error
by fsbuild 31 May '23

31 May '23

External Email - Use Caution Try using $ instead of # to tell the linux shell to expand an environment variable, e.g., here to the path of where freesurfer was installed.   echo $FREESURFER_HOME<output will be path to where installed>   source $FREESURFER_HOME/SetUpFreeSurfer.sh - R. On May 29, 2023, at 07:52, Pedro henrique barradas <phbarradas(a)hotmail.com> wrote:        External Email - Use Caution        Hi everyone!I am trying to run freesurfer on a windows machine using ubuntu but I am having trouble with the source commandWhen I try to source freesurfer i get the following message:source #FREESURFERHOME/SetUpFreeSurfer.sh-bash: source: filename argument requiredsource: usage: source filename [arguments]Thank you very much_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Smoothing with surf2surf
by Akansha Mahesh Naraindas 30 May '23

30 May '23

External Email - Use Caution Hi I have been attempting to perform just the smoothing step on a series of subjects using surf2surf and I seem to be getting an error when attempting to this. My command is as follows mri_surf2surf --hemi lh \ --s fsaverage \ --sval combat_lh-1004.thickness.fwhm0.fsaverage.mgh \ --fwhm 10 \ --cortex \ --tval combatlh.thickness.fwhm10.fsaverage.mgh I get this error ERROR: Option --sval unknown Based on other posts on the mailing list I tried specifying the src and trg subjects but still receive the following error: mri_surf2surf --hemi lh \ --srcsubject fsaverage \ --srcsurfval combat_lh-1004.thickness.fwhm0.fsaverage.mgh \ --fwhm 10 \ --trgsurfval combatlh.thickness.fwhm10.fsaverage.mgh ERROR: Option --srcsubject unknown I was wondering if you might be able to help resolve this issue Thank you very much!

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source freesurfer error
by Pedro henrique barradas 29 May '23

29 May '23

External Email - Use Caution Hi everyone! I am trying to run freesurfer on a windows machine using ubuntu but I am having trouble with the source command When I try to source freesurfer i get the following message: source #FREESURFERHOME/SetUpFreeSurfer.sh -bash: source: filename argument required source: usage: source filename [arguments] Thank you very much

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FS in a HPC cluster via module file: ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer
by Rob Kudyba 26 May '23

26 May '23

External Email - Use Caution In a HPC cluster where freesurfer is loaded ad hoc as a module, running module avail results in the following warning: /path/to/anaconda3-2021.11/bin/mpicc: line 285: x86_64-conda_cos6-linux-gnu-cc: command not found ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer. /path/to/anaconda3-2021.11/bin/mpicc: line 285: x86_64-conda_cos6-linux-gnu-cc: command not found ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer. I don't think ts related but here is my .bashrc file: >>> conda initialize >>> !! Contents within this block are managed by 'conda init' !! __conda_setup="$('/path/to/anaconda3-2021.11/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" if [ $? -eq 0 ]; then eval "$__conda_setup" else if [ -f "/path/to/anaconda3-2021.11/etc/profile.d/conda.sh" ]; then . "/path/to/anaconda3-2021.11/etc/profile.d/conda.sh" else export PATH="/path/to/anaconda3-2021.11/bin:$PATH" fi fi unset __conda_setup The modulefile for Freesurfer contains: module-whatis "adds freesurfer to your environment variables" set root /path/to/freesurfer setenv "FREESURFER_HOME" "/path/to/freesurfer" setenv "SUBJECTS_DIR" "/path/to/freesurfer/subjects" prepend-path PATH $root/bin if { [ module-info mode load ] } { system "source /path/to/freesurfer/SetUpFreeSurfer.sh" } I see that SetUpFreeSurfer.sh has this: # Call configuration script: source $FREESURFER_HOME/FreeSurferEnv.sh After running module unload freesurfer several directories remain in $PATH: echo $PATH /path/to/freesurfer/fsfast/bin:/path/to/freesurfer/tktools:/path/to/freesurfer/mni/bin:/path/to/freesurfer/fsfast/bin:/path/to/freesurfer/tktools:/path/to/freesurfer/mni/bin So $FREESURFER_HOME and $SUBJECTS_DIR are being unset but all of the other env vars are not. Is there a way to unset the vars from FreeSurferEnv.sh? A thread on SO <https://secure-web.cisco.com/1oVSBML06vH3hcXfhl4P1X2gg9xkRWHiWCsxRgOqnwVIMA…> mentions using unsetenv but perhaps there's an elseif that can be added to the modulefile?

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Request for pass code
by Juri Kim 26 May '23

26 May '23

External Email - Use Caution Hi, I am writing to ask if I can get the pass code to open the image to open the FS_7_2_0_ubuntu_18_04_06.ova.7z. Thank you! Sincerely, Juri Kim.

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