Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30128 discussions

Fixing Misclassified Ventricles During QC
by Ran Yan 02 Sep '25

02 Sep '25

External Email - Use Caution Hi Freesurfer team, I am new to FreeSurfer and am currently doing QC using FreeSurfer (v.8). I wanted to check what the best approach is to correcting the following participant (screenshot attached). It appears that the participant had very large ventricles (?), which have been misclassified (as indicated by FreeSurfer drawing the white and pial surfaces around them). My initial thought was to add control points or manually fill the ventricles in WM.mgz, but I wanted to check first, since this issue is widespread across the brain volumes. Many thanks for your help! Sincerely, Rachel -- *Ran (Rachel) Yan* She/her Ph.D. Candidate in Developmental Psychology University of Michigan 530 Church St. | East Hall 2048 | Ann Arbor, MI | 48109-1043

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Re: Docker freesurfer 7.3.2 with MCR for hippocampal subfields
by fsbuild 01 Sep '25

01 Sep '25

External Email - Use Caution  You need to use the fs_install_mcr script to install Matlab inside the freesurfer tree.   The setup is basically the same as listed in the section under SETUP A MATLAB DISTRIBUTION for LINUX except you would replace 8.0.0 with 7.3.2 in the commands.  See,https://secure-web.cisco.com/1IT4xA7-Y5bUYucuGhG4_uwgnX46fM4FVwt37PIUMZbaT2jwRT4nRjx1H7XG6yyLI_377NepxdDj9BHvVwwcOkVr6v5OWXV4v1WTGDnNpp-sW8QVg63GacLKe-Ql3TtjaLIXxGBaW5MQdbPCxyGRr-64pEb1XOI6eCPhsUhgnHM2sqNHXQgXdYt-FvxeGSDbOVm1L3tDDMBhGDK1gp9h2Gvicm_O66e1fwAJDjL-8c-hjiDK1jtai3Hx-Bzr9V6tQ_rq53JVDfxfaNOKojHDTkV7mVWA9gv0DChSK7aBoo7CxZGmC9NDpTRFoY5Tdn-fsmhSeH-uM9fwvhgTPd5e95Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads%2Frel8notes If you can login to the container as root then you do not need to preface the command with sudo.

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Docker freesurfer 7.3.2 with MCR for hippocampal subfields
by Dierker, Donna 01 Sep '25

01 Sep '25

External Email - Use Caution Hi all, Sorry to post on a holiday, but if someone has done this already, and I'm just not finding it, I can use the extra runtime. I'm trying to run segmentHA_T1.sh on some existing freesurfer 7 subject directories using docker image freesurfer/freesurfer:7.3.2, but I'm getting matlab runtime errors. I tried mounting a local MCRv97 library on /usr/local/freesurfer/MCRv97, and I do get a bit further, but I get a different shared library error. Has someone built a docker image that calls fs_install_mcr? Thanks, Donna ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Cortical Thickness From Volume-Space ROIs - Initial Registration Slightly Misaligned
by Rowan Lawrence 27 Aug '25

27 Aug '25

External Email - Use Caution Hello FreeSurfers, We have a number of subjects on which we have run recon-all to completion. We have a number of ROIs for the parahippocampal gyrus (perirhinal, entorhinal, and parahippocampal cortices) defined in volume space on the original T1-weighted images which are registered well, and I would like to extract cortical thickness estimates from these ROIs. I have so far been following the page "Cortical Thickness of a Volume-defined ROI" (https://secure-web.cisco.com/1DVU7ZoSo7uvfZJSPChJydu5jwQ_zDu8idGFGJ4xbpLsX8…) I am using version 8.1.0. I registered the T1 image to the fsaverage image using: fslregister --s fsaverage --mov /mnt/d/.../T1_asl_CON_L01.nii --reg T1_asl_CON_L01_to_fsaverage.dat Which ran without issue. Viewing with the suggested command: tkregisterfv --mov /mnt/d/../T1_asl_CON_L01.nii --reg T1_asl_CON_L01_to_fsaverage.dat --surf orig The registration looks pretty good, although the target structures in the parahippocampal gyrus do not perfectly overlap. Continuing with mri_vol2surf: mri_vol2surf --mov /mnt/d/.../ROIs/T1_asl_CON_L01_L_MTLcROI.mgz --reg T1_asl_CON_L01_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fsaverage.MTLc.mgh And then viewing using the new tksurferfv: tksurferfv fsaverage lh inflated -overlay lh.fsaverage.MTLc.mgh -fthresh 0.5 The ROI appears roughly in the right position, but does not fully overlap the correct gyrus and appears slightly misaligned. Using mri_surf2surf and then writing out the stats with segstats: mri_surf2surf --s T1_asl_CON_L01 --trgsubject fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh mri_segstats --seg lh.fsaverage.MTLc.mgh --in lh.thickness.fsaverage.mgh --sum segstats_MTLc_L.txt The mean thickness is 1mm or less for each of the structures, which does not seem to be correct as manually checking the thickness of parts of the ROIs using measurement tools like ITK-Snap indicates the more expected thickness of ~2.5 - 3.0mm. I assume this must be due to the slightly misaligned ROI when viewed on the fsaverage brain. I have checked other posts on the mailing list and found the suggestion to specify --dof 12 when running fslregister. However, this made the issue considerably worse with the ROI now located in the brainstem and in entirely the wrong orientation. I'm confused about why this has happened and how to fix either issue. Thank you, any help greatly appreciated! Best wishes, Rowan ~ GTA/PhD Candidate School of Health Sciences Booth St. East, 4.034 - M13 9SS

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[FreeSurfer] Different results for T1 vs T2 preprocessing (recon-all 7.4.1, Ubuntu 22.04)
by 이준혁 25 Aug '25

25 Aug '25

External Email - Use Caution Hello FreeSurfer team, I am preprocessing the IXI dataset and noticed that my T2 results look incorrect, even when I run the same pipeline as for T1 with only the input changed to the T2 file. I would appreciate guidance on what I’m doing wrong or how I should process T2 properly. Environment - OS: Ubuntu 22.04.5 LTS - FreeSurfer: 7.4.1 - SUBJECTS_DIR: /mnt/e/freesurfer_subjects - FSF_OUTPUT_FORMAT: nii.gz (default unless noted) What I ran - For a single subject, I tried: input="/mnt/e/T2_all/12subject_12.nii.gz" sid="subject_12T2" outdir="/mnt/e/output" 1) recon-all stage 1 recon-all -parallel -i "$input" -autorecon1 -subjid "$sid" 2) Apply Talairach transform mri_convert "$SUBJECTS_DIR/$sid/mri/brainmask.mgz" --apply_transform "$SUBJECTS_DIR/$sid/mri/transforms/talairach.xfm" -o "$SUBJECTS_DIR/$sid/mri/brainmask_align.mgz" 3) Convert to NIfTI mri_convert "$SUBJECTS_DIR/$sid/mri/brainmask_align.mgz" "$outdir/${sid}_brainmask_align.nii.gz" Issue - The T2 result looks abnormal (while T1 looks OK). I assumed I could reuse the exact same steps for T2, just swapping the input file. - Additionally, when I follow the steps from this guide: https://secure-web.cisco.com/1E1tkmifDB72D9Pbo3i9gNVonTconZI613a_nQKLd5pOD7… my output NIfTI “info” (dimensions, sform/qform, etc.) is slightly different from the author’s preprocessed files (e.g., they have 160×192 while mine often become 256×256×256 after conformation). I’d like to understand why. Questions 1) Is it correct that FreeSurfer’s recon-all is primarily designed for T1, and that T2 should NOT be run through the same standalone pipeline? 2)Then, how can I preprocess T2 using the same code as T1? Is there another method within FreeSurfer to handle T2 properly? 3) “Could you explain why some of the ‘info’ fields differ between the author’s preprocessed files and my outputs, even though I followed the same code?” Thank you very much for your time and guidance! Best regards, [JHL]

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Results of Freesurfer 8.1.0 & Synthseg sometimes deviate by a factor of 1000
by Steinbacher Jürgen 22 Aug '25

22 Aug '25

External Email - Use Caution Hello, I had the problem already with FS 7.2.0, but since it also occurs in FS 8.1.0, which I currently have installed on UBUNTU 20.24, an answer would be helpful. I am fully aware that FS and Synthseg do not provide exactly the same results when calculating the volumes for the same T1 scan with FS and Synthseg. E.g when I calculate a T1 3D 1mm ISO scan and a FLAIR 3D 2mm ISO scan of the same person both with Synthseg, I also fully understand that the results will not be exactly the same here either. However, what I do not understand is that the results for sub-volumes sometimes deviate by a factor of 1000? I have attached a small table below: row 1 Synthseg T1 scan, row 2 Synthseg FLAIR scan, row 3 FS T1 scan same subject. E.g. for "left lateral ventricle," the Synthseg FLAIR and FS results are about the same, but the Synthseg T1 does not match by a factor of 1000. For "left inferior lateral ventricle," the Synthseg FLAIR result is too large. Where do these deviations come from? Is it a unit problem??? I do not understand what is behind it. These deviations occur in all individuals in this manner. Thank you for your help, Jürgen subject total intracranial left cerebral white matter left cerebral cortex left lateral ventricle left inferior lateral ventricle left cerebellum white matter left cerebellum cortex left thalamus left caudate left putamen left pallidum 3rd ventricle 4th ventricle brain-stem left hippocampus left amygdala csf left accumbens area Syn= 02_t1_5_13 1581149.5 234530.16 279514.53 28584312 515.05 15703237 62220.02 5994828 3766241 4605884 1485176 1864659 2365228 23305277 3743831 1692543 258776.8 679.45 Syn= 02_flair_5_13 1540067.8 237580.17 278995.16 26533.9 462551 14112386 64456.68 6460912 3999.81 4585682 1717103 1535.82 1356496 26397467 3787048 1596163 211639.08 720396 fs= 02_t1.5.3 1558777.000000 212518.500000 248086.368363 30058.0 1061.2 16326.6 57684.7 5877.0 3879.4 4342.9 1751.2 2113.8 2982.3 20526.8 4015.2 1763.8 374287.9 539.0 ok ok ok ? ? ? ok ? ? ? ? ? ? ? ? ? ok ?

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Re: New Install on Mac OSX Freeview crashes
by fsbuild 21 Aug '25

21 Aug '25

External Email - Use Caution  Hello Markus, I don’t expect 5.3.0 to work correctly on a new silicon Mac so I would delete 5.3.0 from the new machine.  If you need to continue to do work with and/or verify results with 5.3.0, then continue to run it on your old Intel Mac. Unfortunately, the video you watched is somewhat out of date; it may not work on a silicon Mac with a newer version of MacOS to launch freeview via the Finder so you should try the command line instead (see below). The most recent info on Freesurfer updates is on,https://secure-web.cisco.com/1DjXjsw34RezA-edtO43ClMq-sDvYT3YWxP1tFdi5p6… In the section describing the 8.1.0 release, the “here” link for setup information points to,https://secure-web.cisco.com/1qWt-K1kG7BRaHmR_9Bk17_vSdjMnoSK2jE4ApMMMz2… You should setup your license file to be found in the shell environment via the FS_LICENSE environment variable as described in the 1st section SEETUP FREESURFER LICENSE The section further down the page in SETUP A MATLAB DISTRIBUTION for MACOS lists how you should set the freesurfer environment.  Please try running the bash shell as listed, and I’ve essentially listed all that below.  Once the bash shell output resembles the below, try running freeview from the command line. - R.. - - - - - - …. create a new terminal window and run the bash shell … in the output below the users home directory ($HOME) is /Users/me ... me@MyMac ~ % bash The default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://secure-web.cisco.com/1IrAFVxZF8HFEyYf959stStn-sINjrAkNzOqg-vYOo1Gkx… me@MyMac:~$ export FREESURFER_HOME=/Applications/freesurfer/8.1.0 me@MyMac:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_arm64-8..1.0-20250718-f30dfed --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/8.1.0FSFAST_HOME       /Applications/freesurfer/8.1.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/8.1.0/subjectsMNI_DIR           /Applications/freesurfer/8.1..0/mni …. if you setup FS_LICENSE as listed via the instructions in the setup section of the URL listed above, you should see … me@MyMac:~$ echo $FS_LICENSE/Users/me/license.txt me@MyMac:~$ ls $FS_LICENSE/Users/me/license.txt … test running freeview ... me@MyMac:~$ which freeview/Applications/freesurfer/8.1.0/bin/freeview … make sure an empty window opens … me@MyMac:~$ freeview … if that worked, then try loading a volume … me@MyMac:~$ freeview  $FREESURFER_HOME/subjects/cvs_avg35/mri/brain.mgz You can ignore any notifications about methods/classes w.r.t window functions.

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Re: RHEL / Rocky 9 support
by fsbuild 21 Aug '25

21 Aug '25

External Email - Use Caution  You could try running a rocky8 OS in a singularity, docker, etc. container and then install the FS 8.1.0 rocky8 release in that.  I assume Rocky Linux supports quemu, which should allow running a VM running Rocky 8 linux.  The VM might be a more straightforward option for freeview users (which needs an X-Windows server). - R.

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Re: New Install on Mac OSX Freeview crashes
by Markus Gschwind 20 Aug '25

20 Aug '25

External Email - Use Caution It is me again! I meanwhile have found that I was missing the licence.txt file (it was not mentioned at that stage in the video). However, it seems that it somehow messes up the different versions 8.0.1 and 5.3.0 the shell says this now: -------- freesurfer-macOS-darwin_arm64-8.1.0-20250718-f30dfed -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /Applications/freesurfer/fsfast does not exist FREESURFER_HOME /Applications/freesurfer/8.1.0 FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/8.1.0/subjects MNI_DIR /Applications/freesurfer/mni WARNING: MINC_BIN_DIR '/Applications/freesurfer/mni/bin' does not exist. WARNING: MINC_LIB_DIR '/Applications/freesurfer/mni/lib' does not exist. FSL_DIR /Applications/fsl Therefore I am not sure how to disentangle the versions. Should I just delete the whole 5.3.0? FREESURFER_HOME is set to /Applications/freesurfer/8.1.0 however, why does it not finde the right FSFAST_HOME etc.? Thank you in advance! Markus On Wed, Aug 20, 2025 at 10:03 PM Markus Gschwind <markus.gschwind(a)gmail.com> wrote: > Dear experts, > > After 10 long years, I needed to reinstall FS on a new Mac (M3, running > Sonoma 14.6.1) > > I followed the nice video > https://secure-web.cisco.com/1pQUoPxp0Jn8y34GG4ZV-O7mpRrazzS59AXLr4MQCUn_fy… > (thank you!) > > and I downloaded the freesurfer-macOS-darwin_arm64-8.1.0.pkg > > However, when I try to load a volume into Freeview, it crashes. > > When starting Freeview from a Terminal, it crashes too, saying > > /Applications/freesurfer/8.1.0/bin/freeview: line 2: 87707 Segmentation > fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > > Could anyone please guide me to correct the problem? > Thank you in advance! > Best regards > Markus >

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New Install on Mac OSX Freeview crashes
by Markus Gschwind 20 Aug '25

20 Aug '25

External Email - Use Caution Dear experts, After 10 long years, I needed to reinstall FS on a new Mac (M3, running Sonoma 14.6.1) I followed the nice video https://secure-web.cisco.com/1vGHacmgs-MdkkWjxuHZMMNq48_myOg-DOSd3X_WyADx2h… (thank you!) and I downloaded the freesurfer-macOS-darwin_arm64-8.1.0.pkg However, when I try to load a volume into Freeview, it crashes. When starting Freeview from a Terminal, it crashes too, saying /Applications/freesurfer/8.1.0/bin/freeview: line 2: 87707 Segmentation > fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" Could anyone please guide me to correct the problem? Thank you in advance! Best regards Markus

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