Freesurfer March 2025

freesurfer@nmr.mgh.harvard.edu

49 participants
63 discussions

Using HCP-MMP1 (Glasser) atlas with freesurfer
by Blum, August 04 Mar '25

04 Mar '25

Hi there, I'm on a linux machine, and trying to use the HCP-MMP1 atlas. I tried adding the corresponding .annot file to a freesurfer folder on a /usr/local/freesurfer filepath. However, my computer stated that I don't have permission. Let me know what I can do and if there's any more information that you need! Thank you, August Blum Clinical Research Coordinator I Early Brain Development Initiative Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129

1 0

News: subregion probabilistic atlases in MNI space available
by Iglesias Gonzalez, Juan E. 03 Mar '25

03 Mar '25

Hi everyone, People have asked me to do this multiple times, and I finally got down to it: I put the subregion atlases (hippocampal subfields, nuclei of the amygdala, brainstem subregions, thalamic nuclei) in MNI/ICBM152 space. Details here: https://surfer.nmr.mgh.harvard.edu/fswiki/SubfieldAtlasesICBMspace Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com

1 0

illegal instruction - core dumped with samseg lesion
by Paola Di Filippo 03 Mar '25

03 Mar '25

External Email - Use Caution Hi everyone, I am using freesurfer v. 7.4.1 on a VM and I am trying to run samseg for an MS patient with the following command, but I get the following error: illegal instruction - core dumped. -------- 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:~$ run_samseg --input /home/paolasofia/DICOM.ANG.CHER.2.4.91/NIFTI/A.C.2.4.91.MRI.12.9.22.T1.nii /home/paolasofia/DICOM.ANG.CHER.2.4.91/NIFTI/A.C.2.4.91.MRI.12.9.22.FLAIR_reg.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/paolasofia/LESION.SEG/A.C.2.4.91.MRI.2.9.22.LESIONS/ Illegal instruction (core dumped) any ideas on how I could solve the problem? thanks in advance --

1 0

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer March 2025