Freesurfer January 2025

freesurfer@nmr.mgh.harvard.edu

44 participants
67 discussions

preparing config file for Tracula
by Barletta, Valeria 02 Jan '25

02 Jan '25

Dear Freesurfers, I am setting up the configuration file to run Tracula preproc. I have some doubts on some variables... * pedir: on my DTI protocol I have "PhaseEncodingDirection": "j-",so I assume it is AP * epifactor : I took it from "EchoTrainLength": 48 * echospacing: shall I take it from "DwellTime": 2.5e-06? Should that be indicated in seconds or milliseconds? Thank you, Valeria

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Re: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link 'lh.white.H': Operation not permitted"
by fsbuild 02 Jan '25

02 Jan '25

External Email - Use Caution  Hello Pei-Ying,  It does not work to run freesurfer/recon-all command(s) on subject data that lives on a Windows formatted drive (in your case visible from inside the Linux VM via the mount point to drive d, /mnt/d).   The SUBJECTS_DIR needs to point to a path in the VM Linux filesystem since Windows file systems, e.g., NTFS,  do not support symbolic linking of files.  One way to do that is to put your subject data under your home directory in the Linux VM. $ cd $HOME$ mkdir subject_data… copy in your data to process from /mnt/d …… setup the freesurfer environment as usual by setting FREESURFER_HOME and source the shell init file …… then change SUBJECTS_DIR to point the new location in your Linux $HOME directory ...$ export SUBJECTS_DIR=$HOME/subject_data - R. On Jan 1, 2025, at 22:17, 蔡佩穎 <pcai903(a)gmail.com> wrote:        External Email - Use Caution        Dear FreeSurfer Team, I am attempting to run Recon-all on my data from my research institute, using WSL Ubuntu22.04.5 LTS. On my first attempt to run Recon-all, I got the error shown below: #@# Curv .H and .K rh Thu Jan  2 00:06:17 CST 2025 /mnt/d/suicide/Raw_UD/UD001/surf  mris_curvature -w -seed 1234 rh.white.preaparc rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K  mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated cd /mnt/d/suicide/Raw_UD/UD001/surf reconbatchjobs /mnt/d/suicide/Raw_UD/UD001/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 5816 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5819 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5822 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5825 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5828 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5831 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete.... Waiting for PID 5834 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5837 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5840 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5843 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5846 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5849 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete...  mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 12.423*4pi (156.109) --> -11 handles ICI = 177.4, FI = 1660.9, variation=26709.915 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...mris_curvature done.  rm -f lh.white.H  ln -s lh.white.preaparc.H lh.white.H ln: failed to create symbolic link 'lh.white.H': Operation not permitted  rm -f lh.white.K  ln -s lh.white.preaparc.K lh.white.K ln: failed to create symbolic link 'lh..white.K': Operation not permitted  mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 154 vertices thresholded to be in k1 ~ [-0.54 0.37], k2 ~ [-0.15 0.16] total integrated curvature = 0.361*4pi (4.532) --> 1 handles ICI = 1.5, FI = 8.8, variation=154.684 133 vertices thresholded to be in [-0.04 0.03] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 133 vertices thresholded to be in [-0.22 0.14] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.023 mris_curvature done.  mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 23.152*4pi (290.942) --> -22 handles ICI = 182.8, FI = 1734.3, variation=27614.160 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...mris_curvature done.  rm -f rh.white.H  ln -s rh.white.preaparc.H rh.white.H ln: failed to create symbolic link 'rh.white.H': Operation not permitted  rm -f rh.white.K  ln -s rh.white.preaparc.K rh.white.K ln: failed to create symbolic link 'rh.white.K': Operation not permitted  mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 157 vertices thresholded to be in k1 ~ [-0.46 0.97], k2 ~ [-0.22 0.16] total integrated curvature = 0.314*4pi (3.949) --> 1 handles ICI = 1.4, FI = 9.6, variation=164.776 152 vertices thresholded to be in [-0.07 0.03] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 107 vertices thresholded to be in [-0.21 0.22] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.024 mris_curvature done. PIDs (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) completed and logs appended. Linux DESKTOP-M947IPI 5.15.167.4-microsoft-standard-WSL2 #1 SMP Tue Nov 5 00:21:55 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux recon-all -s UD001 exited with ERRORS at Thu Jan  2 00:06:41 CST 2025 I tried following one of the suggestions in the archives: Method one  /usr/local/freesurfer/7.4.1/subjects drwxr-xr-x 14 root root 4096 Dec 31 16:45 /usr/local/freesurfer/7.4.1/subjects udo chown -R bml-4090:bml-4090 /usr/local/freesurfer/7.4.1/subjects ls -ld /usr/local/freesurfer/7.4.1/subjects drwxr-xr-x 14 bml-4090 bml-4090 4096 Dec 31 16:45 /usr/local/freesurfer/7.4.1/subjects Method two bml-4090@DESKTOP-M947IPI:~$ ls -l lh.white.H lrwxrwxrwx 1 bml-4090 bml-4090 19 Jan  1 21:03 lh.white.H -> lh.white.preaparc.Hbml-4090@DESKTOP-M947IPI:~$ ls -l rh.white.H lrwxrwxrwx 1 bml-4090 bml-4090 19 Jan  1 21:02 rh.white.H -> rh.white.preaparc.H bml-4090@DESKTOP-M947IPI:~$ ls -l rh.white.K lrwxrwxrwx 1 bml-4090 bml-4090 19 Jan  1 21:02 rh.white.K -> rh.white.preaparc.K bml-4090@DESKTOP-M947IPI:~$ ls -l lh.white.K lrwxrwxrwx 1 bml-4090 bml-4090 19 Jan  1 21:02 lh.white.K -> lh.white.preaparc.K How can I allow symbolic links? Thank you so much for your help!Happy new year! Best wishes, Pei-Ying <recon-all.log>

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Recon-all Error: "ln: failed to create symbolic link 'lh.white.H': Operation not permitted"
by 蔡佩穎 01 Jan '25

01 Jan '25

External Email - Use Caution Dear FreeSurfer Team, I am attempting to run Recon-all on my data from my research institute, using WSL Ubuntu22.04.5 LTS. On my first attempt to run Recon-all, I got the error shown below: #@# Curv .H and .K rh Thu Jan 2 00:06:17 CST 2025 /mnt/d/suicide/Raw_UD/UD001/surf mris_curvature -w -seed 1234 rh.white.preaparc rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated cd /mnt/d/suicide/Raw_UD/UD001/surf reconbatchjobs /mnt/d/suicide/Raw_UD/UD001/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 5816 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5819 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5822 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5825 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5828 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5831 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5834 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5837 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5840 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5843 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5846 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5849 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 12.423*4pi (156.109) --> -11 handles ICI = 177.4, FI = 1660.9, variation=26709.915 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...mris_curvature done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: failed to create symbolic link 'lh.white.H': Operation not permitted rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K ln: failed to create symbolic link 'lh.white.K': Operation not permitted mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 154 vertices thresholded to be in k1 ~ [-0.54 0.37], k2 ~ [-0.15 0.16] total integrated curvature = 0.361*4pi (4.532) --> 1 handles ICI = 1.5, FI = 8.8, variation=154.684 133 vertices thresholded to be in [-0.04 0.03] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 133 vertices thresholded to be in [-0.22 0.14] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.023 mris_curvature done. mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 23.152*4pi (290.942) --> -22 handles ICI = 182.8, FI = 1734.3, variation=27614.160 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...mris_curvature done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H ln: failed to create symbolic link 'rh.white.H': Operation not permitted rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K ln: failed to create symbolic link 'rh.white.K': Operation not permitted mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 157 vertices thresholded to be in k1 ~ [-0.46 0.97], k2 ~ [-0.22 0.16] total integrated curvature = 0.314*4pi (3.949) --> 1 handles ICI = 1.4, FI = 9.6, variation=164.776 152 vertices thresholded to be in [-0.07 0.03] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 107 vertices thresholded to be in [-0.21 0.22] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.024 mris_curvature done. PIDs (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) completed and logs appended. Linux DESKTOP-M947IPI 5.15.167.4-microsoft-standard-WSL2 #1 SMP Tue Nov 5 00:21:55 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux recon-all -s UD001 exited with ERRORS at Thu Jan 2 00:06:41 CST 2025 I tried following one of the suggestions in the archives: Method one /usr/local/freesurfer/7.4.1/subjects drwxr-xr-x 14 root root 4096 Dec 31 16:45 /usr/local/freesurfer/7.4.1/subjects udo chown -R bml-4090:bml-4090 /usr/local/freesurfer/7.4.1/subjects ls -ld /usr/local/freesurfer/7.4.1/subjects drwxr-xr-x 14 bml-4090 bml-4090 4096 Dec 31 16:45 /usr/local/freesurfer/7.4.1/subjects Method two bml-4090@DESKTOP-M947IPI:~$ ls -l lh.white.H lrwxrwxrwx 1 bml-4090 bml-4090 19 Jan 1 21:03 lh.white.H -> lh.white.preaparc.H bml-4090@DESKTOP-M947IPI:~$ ls -l rh.white.H lrwxrwxrwx 1 bml-4090 bml-4090 19 Jan 1 21:02 rh.white.H -> rh.white.preaparc.H bml-4090@DESKTOP-M947IPI:~$ ls -l rh.white.K lrwxrwxrwx 1 bml-4090 bml-4090 19 Jan 1 21:02 rh.white.K -> rh.white.preaparc.K bml-4090@DESKTOP-M947IPI:~$ ls -l lh.white.K lrwxrwxrwx 1 bml-4090 bml-4090 19 Jan 1 21:02 lh.white.K -> lh.white.preaparc.K How can I allow symbolic links? Thank you so much for your help!Happy new year! Best wishes, Pei-Ying

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Re: [Freesurfer] Freesurfer Digest, Vol 250, Issue 15
by 黄月虹 01 Jan '25

01 Jan '25

External Email - Use Caution no such email ，thanks 2025-01-01 05:31:40 freesurfer-request(a)nmr.mgh.harvard.edu 写道： > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://secure-web.cisco.com/1wJAnXMczrqK31YqonoPUvDDVxQtRZHFiy6BMW8aPqBziJ… > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Bug Report for Beta Version of FreeSurfer (8.0.0-beta) > (Zhang, Chaokai) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 31 Dec 2024 21:31:40 +0000 > From: "Zhang, Chaokai" <czhang9(a)wpi.edu> > Subject: [Freesurfer] Bug Report for Beta Version of FreeSurfer > (8.0.0-beta) > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CYYPR01MB86123CBE371264C1997BE739EE0A2(a)CYYPR01MB8612.prod.exchangelabs.com> > > Content-Type: text/plain; charset="us-ascii" > > External Email - Use Caution > > Hello FreeSurfer Developers, > Happy New Year! > > I am currently using the latest beta version of FreeSurfer (freesurfer-linux-ubuntu22_x86_64-8.0.0-beta) and have been impressed by the significant acceleration in the recon-all process. However, I encountered an issue while performing a simple labelization on a T1-weighted sample using mri_watershed. When running the command: > mri_watershed -LABEL T1.mgz T1_label.mgz > > I noticed that the output file (T1_label.mgz) is shifted and does not align with the original T1-weighted sample. To confirm, I ran the same command using the stable version (7.4.1), and the output aligned correctly with the T1-weighted sample. > [cid:image001.png@01DB5BA1.780AAF30] > This is just a bug report and does not require any assistance. I wanted to bring this to your attention. Thank you for your hard work and dedication to improving FreeSurfer. > details of my system: > 1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta > 2) Platform: Ubuntu 24.04.1 LTS > 3) uname -a: Linux Kai 5.15.167.4-microsoft-standard-WSL2 #1 SMP Tue Nov 5 00:21:55 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux > > Best regards, > Chaokai > >

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How Can I Track Coordinates from NIfTI Raw Files
by 권용현 01 Jan '25

01 Jan '25

External Email - Use Caution Hello, I am conducting research using ECoG. I want to accurately track the location of electrodes. I am inputting data from a NIfTI file (size: 512, 512, 360, 1). I already know the exact electrode location within the NIfTI file, e.g., (182, 274, 260). The x, y, z values of this coordinate correspond to the raw fMRI scan, with x ranging from 0-512, y from 0-512, and z from 0-360. I extracted the --vox2ras matrix from the 001.mgz file using mri_info. I attempted to project the coordinates from the NIfTI file onto the generated pial surface, but I found a significant discrepancy. What I need is not Talairach coordinates, but a precise transformation of the electrode coordinates in the NIfTI space to their exact location on the subject's pial surface. How can I achieve this? Additionally, I noticed that the origin (0,0,0) of the generated pial surface does not align with the anterior commissure (AC). I am curious about the coordinate system of the final mesh – is it simply the voxel-based x, y, z system, or is it in the RAS coordinate system? Thank you. Best regards, Yonghyeon Gwon -- Yongheyon Gwon Interdisciplinary Program in Neuroscience, Seoul National University, Human Brain Function Laboratory, Seoul National University Hospital Seoul, Korea E-mail: gngyong(a)hbf.re.kr , gyh0321(a)naver.com Phone: +82-10-9706-3814

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FreeSurfer 8.0.0-beta: Stack smashing and normalization failures with 7T MP2RAGE data
by Michael Eyre 01 Jan '25

01 Jan '25

External Email - Use Caution Hello I'm processing 7T MP2RAGE data (0.65mm isotropic) with FreeSurfer 8.0.0-beta. I have processed 30 subjects successfully but am encountering two distinct issues for 3 subjects: 1. Stack smashing errors during topology correction for subjects with large defects (sub-06, sub-31): Copy*** stack smashing detected ***: terminated Command terminated by signal 6 This occurs in mris_fix_topology when processing defects with many vertices: sub-06: Left hemisphere, defect 0 with 22,492 vertices sub-31: Right hemisphere, defect 2 with 14,313 vertices sub-06 does not have any obvious brain abnormalities. sub-31 has some white matter abnormalities at the terminal zones of myelination (deep posterior white matter). 2. Normalization failure for another subject (sub-04): Copyerror: MRInormFindControlPoints: could not find enough control points error: MRInormFindControlPoints failed This subject has some very minor scattered white matter abnormalities (perivascular spaces). My recon-all command: export FS_ALLOW_DEEP=1 recon-all -all -subject ${SUBJECT} -sd ${WORK_PATH}/freesurfer8 -hires -i ${WORK_PATH}/${SUBJECT}_uni_masked.nii.gz -T2 ${WORK_PATH}/${SUBJECT}_t2w_registered.nii.gz -T2pial -expert ${EXPERT_FILE} -openmp 20 My EXPERT_FILE contains two lines: mris_inflate -n 100 mris_fix_topology -threads 1 Preprocessing: Data are processed with 3D Gibbs deringing, ANTS DenoiseImage, bias field correction and brain extraction prior to freesurfer. Approaches tried: I have tried running without the EXPERT_FILE, and also tried with additional recon-all flags -3T -gcut -norm1-n 4 -norm2-n 6, without success. Previous successful processing: The same subjects processed successfully with FreeSurfer 7.4.1. System info: Ubuntu 20.04, 64GB RAM, 20 CPUs. Subjects are running in serial not in parallel, and no other processes with significant memory or CPU use are running on the system at the same time. Any suggestions would be greatly appreciated. I have attached the recon-all.log files. Let me know if you need any additional information. Best wishes Mike Eyre Dr Michael Eyre Locum Consultant Paediatric Neurologist, Evelina London Children's Hospital Visiting Research Fellow, School of Biomedical Engineering & Imaging Sciences, King's College London St Thomas' Hospital London SE1 7EH

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Reliability of Optic Chiasm Volume Measurements in FreeSurfer
by Knut J Bjuland 01 Jan '25

01 Jan '25

External Email - Use Caution Dear FreeSurfer experts, I am examining the optic chiasm segmentation in FreeSurfer. How reliable is the volume measurement of the optic chiasm when using FreeSurfer? Best regards Knut Jørgen Bjuland

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Freesurfer January 2025