Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

Please remove me from this email list
by Haniya Saleh 29 Jun '25

29 Jun '25

External Email - Use Caution Please remove myself (hsaleh(a)uoguelph.ca) from this email list. I get flooded with these emails at my work account and this was something I was assisting 3 years ago. There's no unsubscribe option that I can find. Warm Regards, Haniya Saleh ________________________________________________________________ Haniya Saleh | (She/Her) | Managed Desktops Analyst III – Client Productivity Computing & Communications Services (CCS) | University of Guelph Johnston Hall rm. 034 | 45 Trent Ln | Guelph, ON | N1G 1Y4 519-824-4120 Ext. 56713 | hsaleh(a)uoguelph.ca

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SynthSR - T1 3D post-gadoinium vs. T2 FSE 4mm
by Diana Lorenzo 28 Jun '25

28 Jun '25

External Email - Use Caution Dear All, we are running a project on brain morphometry in a clinical sample without brain injury. For most patients, we have both: * T1W isotropic 1mm post-gadolinium * T2W TSE with 4mm axial slices We would like to obtain high-resolution T1 images with SynthSR followed by standard voxel-based and surface-based processing in CAT12. I am wondering which contrast is best suited for our purpose, also considering that our clinical sample has no brain injury and the only blood vessels are enhanced in post-gadolinium sequences. I made some attempts on both sequences for a couple participants and segmented them with CAT12. The overall image quality rating is almost identical. So is the estimate of total intracranial volume, with some differences in grey matter volume estimation (generally smaller in synthetized post-gado sequences vs synthetized T2) and CSF (generally bigger in synthetized post-gado). I haven't checked surface-based metrics. I am quite new to the field, and I really appreciate your help! Best, Lorenzo Lorenzo Diana, PhD PostDoc Advanced Imaging Research (AIR) Group Swiss Paraplegic Research Guido A. Zäch Strasse 4 6207 Nottwil, Switzerland

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Freesurfer installation help
by Jarrar, Nadine 27 Jun '25

27 Jun '25

Good afternoon, I hope this finds you well. I am a research assistant at MGH, recently took the freesurfer course in June, trying to install it on an arm64 M3 chip Mac (OS Sequoia 15.5), 24GB RAM/memory. I followed the online installation guides and troubleshooting for V8.0.0, yet am getting stuck at the "setup and configuration" step: I successfully installed the freesurfer package file but when I enter the commands in a terminal window to "source the freesurfer environment", the terminal either says "zsh: parse error near '\n'" or it says "source: no such file or directory: /Applications/freesurfer/SetUpFreeSurfer.sh". I copy and pasted the full terminal content below (including the error messages). I looked at older online tutorials for installation, one of them had me load a tab in freeview after installation, before sourcing the environment in a terminal. When I tried to load any volume onto freeview, the app immediately quit and generated an error report. Since the same issue happened repeatedly, I copy and pasted the full error report to a word document attached to this email. Do you have any tips, recommendations, or ideas of what could be going wrong with my setup and configuration? Are there any videos I can consult online, or someone I could speak with to get assistance on my specific errors? Thank you for your time! Have a good weekend. Best, Nadine Terminal message: Last login: Fri Jun 27 11:50:08 on ttys000 nadinejarrar@MGB033764 ~ % export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh source: no such file or directory: /Applications/freesurfer/SetUpFreeSurfer.sh nadinejarrar@MGB033764 ~ % export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh source: no such file or directory: /Applications/freesurfer/SetUpFreeSurfer.sh nadinejarrar@MGB033764 ~ % export FREESURFER_HOME=/Applications/freesurfer/8.0.0 source $FREESURFER_HOME/SetUpFreeSurfer.sh export: not valid in this context: /Applications/freesurfer/SetUpFreeSurfer.sh nadinejarrar@MGB033764 ~ % >.... Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/8.0.0 FSFAST_HOME /Applications/freesurfer/8.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/8.0.0/subjects MNI_DIR /Applications/freesurfer/8.0.0/mni ... install either the Matlab R2014b or R2019b runtime environment ... $ which fs_install_mcr /Applications/freesurfer/8.0.0/bin/fs_install_mcr $ sudo FREESURFER_HOME=$FREESURFER_HOME $FREESURFER_HOME/bin/fs_install_mcr R2019b <output deleted> ... set LD_LIBRARY_PATH to point to The Mathworks libraries ... $ export LD_LIBRARY_PATH=$FREESURFER_HOME/MCRv97/runtime/maci64:$FREESURFER_HOME/MCRv97/bin/maci64:$FREESURFER_HOME/MCRv97/sys/os/maci64:$FREESURFER_HOME/MCRv97/extern/bin/maci64 zsh: parse error near `\n' nadinejarrar@MGB033764 ~ % export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh source: no such file or directory: /Applications/freesurfer/SetUpFreeSurfer.sh nadinejarrar@MGB033764 ~ %

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Updates/bug fixes available for the 8.0.0 release
by fsbuild 27 Jun '25

27 Jun '25

External Email - Use Caution Some updates/bug fixes are available for an existing installation of the Freesurfer 8.0.0 release.  The list of files you can update along with a brief comment about the change(s) are: $FREESURFER_HOME/bin/csvprintScript changed to use python3 - values for eTIV should no longer be misreported as 0.00 for data processed with the recon-all command $FREESURFER_HOME/bin/recon-allFixes for options -autorecon1, -nonuintensitycor.  Add flag -no-fix-ga to turn off fixing of gyrus ambiens part of the cortex label. $FREESURFER_HOME/bin/gtmseggtmseg now uses samseg by default $FREESURFERR_HOME/bin/xhemiregModifications to make xhemireg work with 8.0. $FREESURFER_HOME/bin/xcerebralseggtmseg now uses samseg by default $FREESURFER_HOME/bin/post-recon-allgtmseg now uses samseg by default $FREESURFER_HOME/python/packages/gems/SamsegLongitudinal.pyfix parameters to surfa.image.transform() $FREESURFER_HOME/etc/recon-config.yaml Added option -no-fix-ga to turn off fixing of gyrus ambiens part of the cortex label. Please note THESE UPDATES DO NOT CHANGE THE OUTPUT OF THE recon-all COMMAND. If these updates are of interest to you, then please go the 8.0.0 download URL,https://secure-web.cisco.com/15mh8yOb2RWi2iQyUfX1LgM0gB5PobUejtWnQDIeOm… and download the fs8_update.sh script. On MacOS run the script as follows,$ sudo FREESURFER_HOME=/Applications/freesurfer/8.0.0  bash  fs8_updates..sh On CentOS and Rocky8 Linux run the script as follows,$ sudo FREESURFER_HOME=/usr/local/freesurfer/8.0.0-1  bash  fs8_updates.sh On Ubuntu Linux run the scripts as follows,$ sudo FREESURFER_HOME=/usr/local/freesurfer/8.0.0  bash  fs8_updates.sh You will be prompted on the command line as to whether or not you want to install each file, including displaying the description of the change(s) listed above.

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MRI Physicist position available at the Center for Theoretical and Integrative Neuro- and Cognitive Science (THINK) at Ruhr-University Bochum
by Caspar M. Schwiedrzik 27 Jun '25

27 Jun '25

External Email - Use Caution The newly established Center for Theoretical and Integrative Neuro- and Cognitive Science (THINK) at Ruhr-University Bochum, set to commence operations in 2025, invites applications for an MRI Physicist (39.83 hours/week, 100% FTE, permanent position) to join our interdisciplinary research team. THINK is committed to advancing an integrated, mechanistic understanding of cognition through interdisciplinary and transdisciplinary research that bridges levels of analysis from neural circuits to behavior and connects cognitive domains from perception to action. Central to this mission is the combined use of human and animal models, enabling comparative research that uncovers shared and distinct neurocognitive principles. To support this approach, THINK provides cutting-edge research infrastructure, including co-located laboratories for human, rodent, and avian studies; a 3T Siemens Cima.X human MRI scanner with 64-channel EEG and tDCS; a 9.4T Bruker MRI scanner for small animals; multiphoton and live-cell imaging microscopes; a high-performance computing cluster; and standardized data acquisition systems. These facilities enable tightly integrated, collaborative research aimed at translating basic science into innovative applications in intelligent systems, neurorehabilitation, education, aging, and mental health. THINK is embedded within the Research Department of Neuroscience and actively contributes to major research consortia at Ruhr University Bochum, fostering a dynamic, globally connected scientific environment. For more information, visit: http://secure-web.cisco.com/1tNfjMaUrQl2T0LveMji7kbfTo-xGfj_WAv1UP1gZ3PBBT5… The official job ad can be found here: https://secure-web.cisco.com/1nUP_ZEwNmk7VkNyRIeCQMG645x9tZMb_KcK1mdGajm1iw…

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Re: FS 6 matlab runtime and libcurses in docker
by fsbuild 27 Jun '25

27 Jun '25

External Email - Use Caution  End users of the Matlab runtime need to download it directly from the Mathworks web site and agree to whatever the current licensing terms are during the download/install process. - R.

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Re: FS 6 matlab runtime and libcurses in docker
by fsbuild 27 Jun '25

27 Jun '25

External Email - Use Caution Hello Jeanette, Freesurfer 6 was released back in 2017 for CentOS6,https://secure-web.cisco.com/1qAg_caL2ITqoSd4EdvasaCD0R467g8zXSJtKo… We don’t expect the freesurfer 6 distribution (FS6) to entirely work on Rocky8 linux, e..g., you will probably get run time library errors, because the Linux system libraries have been updated to newer (incompatible) versions some 8 years later for more recent versions of Linux such as Rocky8.  The fs_install_mcr script is part of more recent FS7 and FS8 distributions, but is not part of (or supported in) FS6. If you must use FS6, then your best bet is to make a CentOS6 or CentOS7 docker container and run FS6 in that instead, e.g., download and unarchive the tar images from the above link into your CentOS6/CentOS7 docker container.  Or put whatever version of FS6 you have already been running into that (new) container. Then you could subsequently download and install a version of Matlab that supports the version of CentOS6/CentOS7 running in the container.  I’m not sure there is a Matlab run time environment matching those older OS's, but there should be a full version of Matlab. Unless there is work already done with Freesurfer 6 that you need to continue to work on or support with that same version for continuity, then on Rocky 8 linux, e.g., for new work, we recommend you download and run the FS8 rocky8 linux installer from,https://secure-web.cisco.com/1rRWbe99ZqpjzP3febIH36G6i9KHdZ0XgXI5CkUhv… - R. On Jun 25, 2025, at 12:55, Kenley, Jeanette <jkkenley(a)wustl.edu> wrote:        External Email - Use Caution        Hello installation experts. I am creating a docker which runs OS Rocky 8.I am placing FS6 in said docker. I would like to run recon-all with the -hippocampal-subfields-T1(T2) flag, which requires the libcurses libraries. I cannot download and execute this file in the docker successfully because it throws a VM library error when executed.  (I apologize the exact error is no longer available to me)https://secure-web.cisco.com/1FrIuq3tL5KO5-jI1Oe1gFi4SMTOD-zRut9HpuxOnMx… Thus I was attempting to load this file into the docker:https://secure-web.cisco.com/1H8IPq9NQ0AlAR3Mk_yBocmB1PiA1VAT4Abzh_A… Which I planned to subsequently untar and add the libcurses to the MCRv80 output folder, but unlike on 18 June 2025, the file is no longer available. Is there a reason this file was removed?Or do you have a recommendation on how to make the above script run, which then I can add the libcurse libraries to? Thank you for your time.Jeanette The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email.  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._______________________________________________Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.eduTo unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/

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High-resolution Data in FreeSurfer
by Mahta Abbaspour 27 Jun '25

27 Jun '25

External Email - Use Caution Hi, I had a question regarding how FreeSurfer handles high-resolution MRI scans. I understand that it typically accepts isotropic 1 mm scans (and up to 1.5 mm). I wanted to confirm whether using the -hires flag alone is sufficient for processing this type of data, and if there are any additional considerations I should be aware of when reviewing the outputs. I’m using v8.0.0. and working with a dataset acquired at 0.5 × 0.5 × 1 mm resolution. I used the -hires flag with recon-all, and FreeSurfer preserved the resolution and resampled it to isotropic 0.5 mm voxels. Also, does using high-resolution data affect the alignment or reliability of atlas-based parcellations (like Desikan-Killiany), given that those templates were originally developed on standard-resolution scans? Thank you for your help. Best

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Extracting Z score from surface single subject level
by Federica Tomaiuolo 27 Jun '25

27 Jun '25

External Email - Use Caution Hi, I'm experiencing a problem while trying to extract Z score from single subject's z.nii.gz map coming from FSFAST. More in detail, I created different .label files in freeview from the group-level statistics maps (in fsaverage space), each one containing a thresholded z-stat cluster. Then, I wanted to use this label files to extract from each z.nii.gz (still in fsaverage space) single subject's map, the Zscore values corresponding to the ROI associated to the cluster coming from the label. I've always made this process with volume files using FSL, by combing fslmaths and fslstats, but I didn't find a corresponding command in FreeSurfer for surface files. I tried using mri_segstats but I'm not sure is able to work with surface maps. Could someone help me, please? Thank You, Federica Tomaiuolo

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R: Certificate of Partecipation - Virtual FreeSurfer Course
by Giuseppe CIULLO 27 Jun '25

27 Jun '25

External Email - Use Caution Dear Sirs, Could you kindly provide me with the certificate of participation, with my name and surname on, for the last Virtual FreeSurfer course attended two weeks ago? Thank you very much for your support. Best regards, Giuseppe ________________________________ Da: Giuseppe CIULLO Inviato: venerdì 27 giugno 2025 11:51 A: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Oggetto: Certificate of Partecipation - Virtual FreeSurfer Course Dear Sirs, Could you kindly provide me with the certificate of participation, with my name and surname on, for the last Virtual FreeSurfer course attended two weeks ago? Thank you very much for your support. Best regards, Giuseppe

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Freesurfer