Freesurfer

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30070 discussions

ERC_bayesian_segmentation is not shipped in the nightly dev build
by Chourrout, Matthieu 17 Feb '25

17 Feb '25

External Email - Use Caution Hi all, I was trying to run the dev version of FreeSurfer from https://secure-web.cisco.com/1WtBzDJVBe2-2xc-ZyLSEcxaAxh0X5-CzPpHRJlz_acv5L… but the content from https://secure-web.cisco.com/1MMHkQC0FfiJGDyWJmsuvvc_IYxIL5eyKAe0D4iNTL8uZ9… is not present in ${FREESURFER_HOME}/python/packages/ As instructed, I've put atlas_full/ and atlas_simplified/ inside ${FREESURFER_HOME}/python/packages/ERC_bayesian_segmentation/ when trying to run mri_histo_atlas_segment_fireants but had to manually create the subdir. can't open file '/share/apps/freesurfer-dev/python/packages/ERC_bayesian_segmentation//scripts/segment_fireants.py': [Errno 2] No such file or directory Can the files from ERC_bayesian_segmentation/ in GitHub be manually pulled out into this directory? Which files are required? Best regards, Dr Matthieu Chourrout [orcid logo 16px] <https://secure-web.cisco.com/1-n5OFLL4s4yFn7XM1MH7qpzWv10xwrOxrYPwOpqLI0AgP…> Research Fellow on Correlative X-ray Imaging for the Large-scale Imaging of Neural Circuits UCL Mechanical Engineering<https://secure-web.cisco.com/10kRa1voAealTFL-mjMLpqi2JdO0FO-HEtTDRw-L3blsf8…> Materials, Structure and Manufacturing at Harwell (MSMaH)<https://secure-web.cisco.com/1xdgUA8Zer-mG8V0D7hnqtYAAE7M6hmti3ln6qu7pf_60k….> Rm 4.17 Malet Place Eng. Building, Torrington Place, London, WC1E 7JE Bloomsbury Campus, University College London

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Re: [Freesurfer] recon-all failed
by fsbuild 16 Feb '25

16 Feb '25

External Email - Use Caution  You can read from but not write to where freesurfer is installed under /usr/local/freesurfer as your normal userid.   Just change the setting of SUBJECTS_DIR to be, e.g., in your home directory or some location you can always write to as your normal userid.  It’s a good idea not to modify the distribution installed under /usr/local/freesurfer.  To change to your home directory, … setup the freesurfer environment which by default sets SUBJECTS_DIR to be under /usr/local/freesurfer ....$ cd $HOME… or …$ cd$ mkdir subjects$ cd subjects… copy in you subject data …$ export SUBJECTS_DIR=$HOME/subjects…. then re-run your command(s) ... - R. On Feb 15, 2025, at 12:52, Paola Di Filippo <paola.difilippo(a)unifg.it> wrote:        External Email - Use Caution        hi everyone,i have succesfully managed to download freesurfer with ubuntu 22 on a virtual machine. i've tried some tutorials and everything is working fine.now i am trying to run my first recon-all, but this is the error I get: -------- freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /usr/local/freesurfer/7.4.1 FSFAST_HOME       /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /usr/local/freesurfer/7.4.1/subjects MNI_DIR           /usr/local/freesurfer/7.4.1/mni paolasofia@Freesurfer-ub22:~$ recon-all -subject angcher.02.04.91.12.09.22 -sd /usr/local/freesurfer/7.4.1/subjects  -i /home/paolasofia/DICOM.ANG.CHER.2.4.91/DICOM/./1.3.12.2.1107.5.2.19.146011.2022091213511174521774361.dcm -i /home/paolasofia/DICOM.ANG.CHER.2.4.91/DICOM/./1.3.12.2.1107.5.2.19.146011.2022091213511942168418847.dcm -i /home/paolasofia/DICOM.ANG.CHER.2.4.91/DICOM/./1.3.12.2.1107.5.2.19.146011.2022091213511945768618951.dcm -all  mkdir: cannot create directory '/usr/local/freesurfer/7.4.1/subjects/angcher.02.04.91.12.09.22': Permission denied fs-check-version --s angcher.02.04.91.12.09.22 --o /tmp/tmp.VZQFHn ERROR: cannot find angcher.02.04.91.12.09.22 recon-all: version check failed fs-check-version --s angcher.02.04.91.12.09.22 --o /tmp/tmp.VZQFHn how could i solve this problem?thanks in advance _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1QY3rGdqJouwjNSkdy2O1DaMbRHvOVLBCmyyP7lydP63wt…

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recon-all failed
by Paola Di Filippo 15 Feb '25

15 Feb '25

External Email - Use Caution hi everyone, i have succesfully managed to download freesurfer with ubuntu 22 on a virtual machine. i've tried some tutorials and everything is working fine. now i am trying to run my first recon-all, but this is the error I get: -------- freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1 FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects MNI_DIR /usr/local/freesurfer/7.4.1/mni paolasofia@Freesurfer-ub22:~$ recon-all -subject angcher.02.04.91.12.09.22 -sd /usr/local/freesurfer/7.4.1/subjects -i /home/paolasofia/DICOM.ANG.CHER.2.4.91/DICOM/./1.3.12.2.1107.5.2.19.146011.2022091213511174521774361.dcm -i /home/paolasofia/DICOM.ANG.CHER.2.4.91/DICOM/./1.3.12.2.1107.5.2.19.146011.2022091213511942168418847.dcm -i /home/paolasofia/DICOM.ANG.CHER.2.4.91/DICOM/./1.3.12.2.1107.5.2.19.146011.2022091213511945768618951.dcm -all mkdir: cannot create directory '/usr/local/freesurfer/7.4.1/subjects/angcher.02.04.91.12.09.22': Permission denied fs-check-version --s angcher.02.04.91.12.09.22 --o /tmp/tmp.VZQFHn ERROR: cannot find angcher.02.04.91.12.09.22 recon-all: version check failed fs-check-version --s angcher.02.04.91.12.09.22 --o /tmp/tmp.VZQFHn how could i solve this problem? thanks in advance --

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Unusual Cortical Thickness Measurements in Specific Regions
by hmarzban＠student.ubc.ca 14 Feb '25

14 Feb '25

External Email - Use Caution Hello developers I am encountering unexpected cortical thickness values in the following regions: lh_G_Ins_lg_and_S_cent_ins_thickness lh_S_intrapariet_and_P_trans_thickness lh_S_oc_middle_and_Lunatus_thickness lh_S_oc-temp_med_and_Lingual_thickness lh_S_oc_sup_and_transversal_thickness Upon calculating the means for these regions, I observed significant differences compared to my control group. However, I am uncertain whether these discrepancies are attributable to the illness under study or to potential segmentation errors. I am seeking advice on steps or considerations to address this issue. Can you provide insights into potential causes and solutions? Thank you for your assistance. Regards Hengameh

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Amygdala nuclei atlas
by Krista Wahlstrom 14 Feb '25

14 Feb '25

External Email - Use Caution Good morning, Freesurfer team! I'm interested in using the amygdala atlas created by Saygin ZM & Kliemann D et al., 2017 (High-resolution magnetic resonance imaging reveals nuclei of the human amygdala: manual segmentation to automatic atlas). I understand this atlas is integrated into the Freesurfer software; however our research team uses an alternative software for human brain imaging processing. I'm wondering if it's possible to gain access to the code for your segmentation of the amygdala so we can implement this atlas into our own imaging processing pipeline. I wasn't able to find the amygdala atlas code on the Freesurfer GitHub, but it's possible I wasn't looking in the correct repository. Any help would be much appreciated! Thanks, Krista **************************************** Krista Wahlstrom, Ph.D. University of Utah Department of Psychology Cognition & Neural Science | CNS Postdoctoral Research Associate INMAN Laboratory<https://secure-web.cisco.com/1j4sHQVeR_3rCIIA29tFpHoNp8Sc-LeT178BzyiKrItw-c…> [cid:120e0f87-08bb-457c-aa0d-d302467fcd28] [cid:a613c0be-3f3e-45da-96b4-05a0c1cf72cb]

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Re: [Freesurfer] freeview runtime error...
by Gonzalo Rojas Costa 14 Feb '25

14 Feb '25

External Email - Use Caution Hi: I tested all the commands that you told me, but, I still have the error that I had specified to you: "gonzalorojascosta@gonzalobrain:~$ freeview This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb. Abortado (`core' generado) gonzalorojascosta@gonzalobrain:~$" Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University

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FreeSurfer coordinates
by Yang Yifan 14 Feb '25

14 Feb '25

External Email - Use Caution Hi FreeSurfer Developers, I’m conducting manual ROI labelling on each participant’s inflated surface (after going through the ‘recon-all’ command), but I wasn’t very sure if the coordinates in the corresponding .label files are in MNI 305 space. At the top of the plain text files it’s showing ‘vox2ras=TkReg’. If they are not in MNI 305, could you please explain a bit about what coordinate system is used here and how I could convert that into MNI 305? Thank you very much! Best wishes, Vivian

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Issue with Voxel Size Mismatch in Samseg-Long Pipeline
by Taghizadeh Mortezaei, Nima 14 Feb '25

14 Feb '25

Dear FreeSurfer Team, I am working with two timepoints for a subject and attempting to create a template for samseg-long using mri_robust_template. However, I encountered an error related to voxel size mismatch between the input images. Both timepoint images are T1W. The command I ran is: mri_robust_template --mov subject1_preRT.nii subject1_postRT.nii --template mean.mgz --satit --mapmov subject1_preRT_reg.mgz subject1_postRT_reg.mgz I received the following error: ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.428571, 0.428571, 4.4 size(0) = 0.449219, 0.449219, 5 error: Operation not permitted error: MultiRegistration::loadMovables: voxel size is different subject1_postRT.nii. >From what I understand, mri_robust_template does not support different voxel sizes between input images. Would the recommended approach be to first resample the images to the same voxel size using mri_convert --conform or another method before running mri_robust_template? Additionally, would this resampling introduce any potential biases that I should be aware of in a longitudinal analysis? If there is a better way to handle this issue, I would greatly appreciate your guidance. Best regards, Nima

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Re: [Freesurfer] freeview runtime error...
by fsbuild 14 Feb '25

14 Feb '25

External Email - Use Caution  Try running the bash shell i.e., exec a new bash shell in the terminal window,$ bash I assume you installed the .deb file,https://secure-web.cisco.com/1vpMI_roAst1mdZTXwOe7ZmxVcxxk_NPabzpPTF6Z… from where you downloaded it to with the command ...$ sudo apt install ./freesurfer_ubuntu18-7.4.1_amd64.deb But if you did not run that command, then please do so. Make sure this package is installed. If it is already installed, the system should report there is nothing to do.$ sudo apt install mesa-utils If these 2 environment variables are not already set in your environment, i.e., there is no output listed for them using the echo command,$ echo $XDG_RUNTIME_DIR$ echo $DISPLAY …. then I would try setting them to be ...$ export XDG_RUNTIME_DIR=$HOME/.xdg$ export DISPLAY=:0 Then try running glxgears,$ glxgears If glxgeaqrs does not display rotating gears then there is something still not right with your graphics, display, system settings. If glxgears worked, then setup the freersurfer environment,$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh<output deleted> $ which freeview/usr/local/freesurfer/7.4.1/bin/freeview … then try opening an empty window with freeview …$ freeview If that worked, close the freeview window and try opening one of the provided volumes,$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz If that worked, then try opening one of your own files with freeview. If opening the bert volume file did not work, try setting this environment variable and re-run that command to open that volume,$ export QT_DEBUG_PLUGINS=1$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz … you will see quite a bit of output.  Look towards the end of the output and try to identify what it says is missing or what was not found on the system. - R. On Feb 13, 2025, at 22:55, Gonzalo Rojas Costa <gonzalo.rojas.costa(a)gmail.com> wrote:        External Email - Use Caution        Hi: it is freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460, under Ubuntu 18.04.4 LTS. In a real physical ubuntu. Sincerely, Gonzalo M. Rojas-CostaAdjunct Assistant Professor School of Medicine Finis Terrae University_______________________________________________ Freesurfer mailing list Freesurfer@nmr..mgh.harvard.edu https://secure-web.cisco.com/1VgXhN-f_Nad83y_Z7cLJL7GA2ENYdx-E6OK2zMWYbLOYL…

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Re: [Freesurfer] freeview runtime error...
by Gonzalo Rojas Costa 13 Feb '25

13 Feb '25

External Email - Use Caution Hi: it is freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460, under Ubuntu 18.04.4 LTS. In a real physical ubuntu. Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University

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