Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

Licence for using Freesurfer-generated images in a book?
by ALARIO Francois 12 Jul '24

12 Jul '24

External Email - Use Caution Hello I am considering using freesurfer-generated images not in a scientific paper but in a popular science book (commercial). What is the preferred course of action, license-wise, for this specific purpose? Can I include images of fsaverage with Desikan atlas parcellations, or should I avoid using fsaverage and use instead images I have acquired? The general license is worded in terms of “Software”, but said figures would not appear to laypeople to be “Software” May I skip the words "All or portions of this licensed product (such portions are the "Software") have been obtained under license from The General Hospital Corporation and are subject to the following terms and conditions:" and more plainly acknowledge that the images were created with Freesurfer by citing ''Cortical reconstruction and volumetric segmentation was performed with the Freesurfer image analysis suite, which is documented and freely available for download online (<http://surfer.nmr.mgh.harvard.edu/>)'', along with one of the papers (which one)? The book is in French the recommended option would be translated to French. Any advice would be appreciated. Kind regards Xavier -- Xavier ALARIO + 33 4 13 55 09 72 https://cv.hal.science/f-xavier-alario https://crpn.univ-amu.fr/fr/annuaire/alario-xavier

2 1

Longitudinal Analysis Error
by Ahmet Kaya 10 Jul '24

10 Jul '24

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to perform longitudinal analysis of brain volumes with two timepoints for each patient. Some of these patients were scanned using different scanners. When creating a base file for longitudinal analysis, I encounter the following error: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 rca-base-init 7.4.1 Darwin Kayas-MacBook-Pro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:32:11 PDT 2023; root:xnu-10002.41.9~7/RELEASE_ARM64_T6030 arm64 pid 3979 #-------------------------------------------- #@# Longitudinal Base Subject Creation Sat Jul 6 15:59:22 +03 2024 /Users/kayaacademia/Desktop/MS_LAB/10402969_base \n mri_diff --notallow-pix --notallow-geo /Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/rawavg.mgz /Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/rawavg.mgz \n error: mghRead(/Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/rawavg.mgz, -1): could not open file \n******************************************************************************* WARNING: Image parameters differ across time, maybe due to acquisition changes? Consistent changes in, e.g., resolution can potentially bias a longitudinal study! You can check image parameters by running mri_info on each input image. Will continue in 10 seconds ... *******************************************************************************\n \n mri_robust_template --mov /Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz /Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/norm.mgz --lta /Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/transforms/10402969_19_to_10402969_base.lta /Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/transforms/10402969_22_to_10402969_base.lta --template /Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/norm_template.mgz --average 1 --sat 4.685 \n 7.4.1 --mov: Using /Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz as movable/source volume. --mov: Using /Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/norm.mgz as movable/source volume. Total: 2 input volumes --lta: Will output LTA transforms --template: Using /Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/norm_template.mgz as template output volume. --average: Using method 1 for template computation. --sat: Using saturation 4.685 in M-estimator! reading source '/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz'... error: mghRead(/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz, -1): could not open file error: MultiRegistration::loadMovables: could not open input volume /Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz. ERROR: Darwin Kayas-MacBook-Pro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:32:11 PDT 2023; root:xnu-10002.41.9~7/RELEASE_ARM64_T6030 arm64 recon-all -s 10402969_base exited with ERRORS at Sat Jul 6 15:59:33 +03 2024 I have attached the recon-all.log file for your reference. I am not a data scientist and am unable to determine the cause of this issue. I would greatly appreciate your guidance on how to resolve this error. 1. *FreeSurfer version:* freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 2. *Platform:* macOS 23.1.0 3. *uname -a:* Darwin Kayas-MacBook-Pro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:32:11 PDT 2023; root .41.9~7/RELEASE_ARM64_T6030 arm64 4. *recon-all.log:* see attached Thank you for your assistance, much appreciated. Best regards, Ahmet Kaya, MD

2 3

BUG: FTP Server data visible without credential
by Kavar Hardik 10 Jul '24

10 Jul '24

External Email - Use Caution Hello FreeSurfer Developers, I am checking your website and I found your FTP server are configured without Credentials. FTP URL: https://surfer.nmr.mgh.harvard.edu/ftp/ POC attached with mail. Regards Kavar Hardik

1 0

Unknown recon-all error - ERROR: reading ../surf/autodet.gw.stats.lh.dat
by Austin Cooper 09 Jul '24

09 Jul '24

External Email - Use Caution Hello there! I'm hoping that someone can resolve this issue which I'm having. To me it seems that the pipeline is looking for ../surf/autodet.gw.stats.lh.dat, and I can confirm that it does not exist. Is there a quick solution? Everything in recon-all was functioning without error up to this point. The error is as follows: mri_vol2vol done #-------------------------------------------- #@# c2hWhiteSurfs lh Thu Jul 4 23:07:31 EDT 2024 cd /project/6001995/Shmuel_Mendola/data/MGH/HCPNaming/control/05_scan1/T1w/05/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg rawavg.aseg.presurf.mgz --wm rawavg.wm.mgz --invol rawavg.brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc.rawavg --o ../surf/lh.white.rawavg --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-wmsa --rip-surf ../surf/lh.white.preaparc.rawavg --aparc ../label/lh.aparc.annot ERROR: reading ../surf/autodet.gw.stats.lh.dat ERROR: Linux bc11246.int.ets1.calculquebec.ca 4.18.0-513.24.1.el8_9.x86_64 #1 SMP Thu Apr 4 18:13:02 UTC 2024 x86_64 GNU/Linux recon-all -s 05 exited with ERRORS at Thu Jul 4 23:07:32 EDT 2024 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Yours truly, Austin Cooper BEng - University of Guelph PBD - Cognitive Science - Carleton University PhD Candidate - Neuroscience - McGill University

2 1

LME model error: mris_average_surface failed
by Bondi, Daniel 09 Jul '24

09 Jul '24

External Email - Use Caution Hello, I am trying to test the LME model created by Bernal using mass-univariate data. Although my entire dataset has about 40 participants with pre- and post-season scans, I am trying to test the pipeline with the data from one subject. On my Mac, I am unable to run “make_average_subject” for the test subject successfully without error. The error message is “ERROR: creating directory / mri_average_surface failed”. Freesurfer is able to create a directory within the subject folder on my desktop (study_average) but can’t make a “surf” folder within that. When I run sudo before this command, the error is “FREESURFER_HOME: undefined variable” even though I have it defined in my bash profile and echoing it shows /Applications/freesurfer/7.3.2. I was on Freesurfer 7.2.0 originally, but I’ve now upgraded to 7.3.2 to fix this error but had no luck. I’ve also changed all the read/write permissions in the file directories but still no luck. Thanks, Daniel

1 0

freeview colormap for volumes
by Proulx, Jean Sebastien 09 Jul '24

09 Jul '24

Hello, This seems to be a longstanding issue, unless there is a post I miss. How can one specify a custom colormap for a volume? Bonus point for how to specify an alpha channel for voxel-specific transparency. My immediate goal: visualize angle data with a colorbar that wraps around a full circle (same color for values 0 and 2pi). That would be enough for now, but ultimately I want these angles to display with high transparency for voxels where the estimate is uncertain (low 2-d vector magnitude). Thanks for the help and Have a great day! Sebastien

2 1

Re: [Freesurfer] Not able to install Matlab Runtime (MCR)
by fsbuild 09 Jul '24

09 Jul '24

External Email - Use Caution  It looks like /tmp is running out of space (which can be a separate partition much smaller than the boot partition) to the point where the matlab installer cannot use it.  You can check that with, $ cd /tmp$ df -h . You should be able to delete anything under /tmp as nothing permanent should be written there. - R. On Jul 9, 2024, at 04:02, Himanshu Joshi <anshuhim20(a)gmail.com> wrote:        External Email - Use Caution        Dear list,I am trying to install matlab runtime environment (MCR) in $FREESURFER_HOME/freesurfer by using fs_install_mcr R2019b. the error is mentioned below: (Jul 09, 2024 12:00:11) The following error was detected while installing 3p/mpich2_glnxa64: /tmp/tmp.YZJEtKG8O6/install-target/v97/bin/glnxa64/smpd (No space left on device) Would you like to retry installing 3p/mpich2_glnxa64?  If you press No, the installer will exit without completing the installation.  More information can be found at /tmp/mathworks_MBIAL.log (Jul 09, 2024 12:00:11) Exiting with status -1 (Jul 09, 2024 12:00:11) End - Unsuccessful. Finished R2019b installed successfully in /home/MBIAL/freesurfer/MCRv97 We have enough space on / filesystem: Filesystem             Size  Used Avail Use% Mounted on /dev/mapper/rhel-root   50G   43G  7.4G  86% / devtmpfs               252G     0  252G   0% /dev tmpfs                  252G   21M  252G   1% /dev/shm tmpfs                  252G   19M  252G   1% /run tmpfs                  252G     0  252G   0% /sys/fs/cgroup /dev/sda2              497M  219M  279M  44% /boot /dev/mapper/rhel-home  3.3T  2.3T  961G  71% /home tmpfs                   51G   48K   51G   1% /run/user/1003 Kindly suggest the needful Thanks and Regards --  Dr Himanshu Joshi _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Not able to install Matlab Runtime (MCR)
by Himanshu Joshi 09 Jul '24

09 Jul '24

External Email - Use Caution Dear list, I am trying to install matlab runtime environment (MCR) in $FREESURFER_HOME/freesurfer by using *fs_install_mcr R2019b*. the error is mentioned below: (Jul 09, 2024 12:00:11) The following error was detected while installing *3p/mpich2_glnxa64:/tmp/tmp.YZJEtKG8O6/install-target/v97/bin/glnxa64/smpd (No space left on device)* Would you like to retry installing 3p/mpich2_glnxa64? If you press No, the installer will exit without completing the installation. More information can be found at /tmp/mathworks_MBIAL.log (Jul 09, 2024 12:00:11) Exiting with status -1 (Jul 09, 2024 12:00:11) End - Unsuccessful. Finished R2019b installed successfully in /home/MBIAL/freesurfer/MCRv97 We have enough space on / filesystem: Filesystem Size Used Avail Use% Mounted on /dev/mapper/rhel-root 50G 43G 7.4G 86% / devtmpfs 252G 0 252G 0% /dev tmpfs 252G 21M 252G 1% /dev/shm tmpfs 252G 19M 252G 1% /run tmpfs 252G 0 252G 0% /sys/fs/cgroup /dev/sda2 497M 219M 279M 44% /boot /dev/mapper/rhel-home 3.3T 2.3T 961G 71% /home tmpfs 51G 48K 51G 1% /run/user/1003 Kindly suggest the needful Thanks and Regards -- Dr Himanshu Joshi

1 0

Is ICV needed as a covariate if matched between groups
by Carly McIntyre-Wood 08 Jul '24

08 Jul '24

3 2

Robustness of Segmentation and Parcellation to Lesions
by Hickman, Leonard B. MD 05 Jul '24

05 Jul '24

External Email - Use Caution Hello all, I am using FreeSurfer to measure specific cortical parcellations and subcortical segmentations in a medium-sized dataset (over 150 scans). About a fifth of the scans include cortical lesions (ischemic stroke, hemorrhagic stroke, focal traumatic injuries, neoplasm) that visibly disrupt recon-all's white matter surface and the pial surface locally at the lesion. Assuming there is no midline shift, does the recon-all processing stream perform segmentations and parcellations in each hemisphere independently? Or, could a unilateral lesion impact segmentation/parcellation on the contralateral side? For segmentation/parcellation measurements on the side ipsilateral to a lesion, how robust are recon-all's measurements in non-lesioned regions? For instance, are hippocampal volume measurements impacted by a cortical lesion in the frontal convexity? Or a lesion in a lateral temporal gyrus? Are there any general guides on how close a lesion can be to a ROI before automated measurements are invalid? Thank you much in advance, Brian -- L. Brian Hickman, MD, MSc ________________________________ UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer