Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30063 discussions

7.4.0 Recon-all_Clinical - error in computing lh.BA_exvixo.annot
by NicolasNorton 02 Jun '23

02 Jun '23

External Email - Use Caution Hey Devs, I'm experimenting with recon-all_clinical in FS 7.4.0. I'm wondering how to pass the --qcache option to recon-all. I also wanted to give you a heads up that recon-all_clinical is calling for a colortable in the dev build which is resulting in an error. I don't think this will affect my analysis but it may someone else's. Here is the error message: " ERROR: cannot find or read /usr/local/freesurfer/dev/average/colortable_BA.txt computing statistics for each annotation in ./lh.BA_exvivo.annot. " Its the same for RH.BA_exvivo.annot, and continues: error: No such file or directory error: could not read annot file ./rh.BA_exvivo.annot error: No such file or directoryerror: mris_anatomical_stats: could not read annotation file ./rh.BA_exvivo.annot Please let me know if this will affect thickness or volume analysis. Thanks, Nic

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Freesurfer installation
by Stefan Rampp 02 Jun '23

02 Jun '23

External Email - Use Caution Dear Freesurfer developers, For the installation of Freesurfer, I'd need a pass code to extract the zip file. Best regards Stefan

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Re: [Freesurfer] Sourcing freesurfer
by fsbuild 01 Jun '23

01 Jun '23

External Email - Use Caution Hello Pedro, It does not look like you are using a standard installation of freesurfer given the path you list below as /root/freesurfer. We have information available about how to use either WSL (Windows Subsystem for Linux) to host Ubuntu Linux in order to run Freesurfer on Windows, https://secure-web.cisco.com/1kqIIthfElwIFp4xfRtH02uxDl8MR86sRRP-ugqp0vSmGT… - or you can install VirtualBox on your Windows machine to run a VM we provide for download with freesurfer already installed and setup to run (see https://secure-web.cisco.com/1v32HavIAAMjouxecLl5yEhLk0tyE2hxIHnDGZC-o-FlJl…) For WSL, once you have Ubuntu Linux running, we recommend using one of the debian (.deb) package installers listed on the Freesurfer 7 download page that matches your Ubuntu system (https://secure-web.cisco.com/1q0Hyt7h01b-vvXLm4oWRsX0bWB4JcKCG1QCz9R_lYE6XH… So for Ubuntu 22 running in WSL, you would download one of the freesurfer_ubuntu22-7.X.X_amd64.deb files into Ubuntu linux and install it.  That would install freesurfer as /usr/local/freesurfer/7.x.x in the Ubuntu Linux image running in WSL.    In the VM, freesurfer 7.2.0 is already installed as /usr/local/freesurfer/7.2.0 We recommend you verify you are using (or try) one of the setups above. - R. On 6/1/23 11:38, Pedro henrique barradas (phbarradas(a)hotmail.com) wrote:         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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1rCsMjiZIFhaEwoY93DEQzlsfPXVd-HIQ12aABmwCyfvS7… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/118-9oU96FBuN-fAsM44xOA0MwIfhdZwbjRCeoLflO_wr8… <https://secure-web.cisco.com/1dNhjMyd4TYc8nsrgllD7hrTFSK1vGTJjsNEAy5RvBAj2dcZVIqKezDjWV9AEXSi_Zgf1TS6Sm0FM6GmczEq96Yp_42KH1GvUHTqu2ym0RhSRt9ZU7QGgxTSzAxbuwuWkZjcb0MjUZOnrMEeDrLeod_AOz610_wNhQuA0380mlMtXwof-BUBefkW8mBPiB785MTI_PkZWIz2iKb4YOD6jr7ql3lCnJ0oV63_Nzg4UZH9lEPP9v-1l11BZH-fuIMFAjV-BP-Jup0HYvlzF7dOMUrdXWtYzPeiUALcojMg5ZKSF4Za0hRjEw2KQjIGez0fTFFN8xZ3LtGigUpUHU485Pw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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[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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