Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

Longitudinal Stream Error
by Willett, Andrew Sunday 13 Feb '22

13 Feb '22

This is my first time seeking support here so I apologize if I am not familiar with the community's conventions. I am encountering errors when processing Freesurfer longitudinal stream (Freesurfer v6.0). Cross-sectional streams proceeded and completed without error, but base template creation and all following longitudinal steps failed. I created a txt script for the base template creation: Here is a sample: module load freesurfer export FREESURFER_HOME=/.../.../freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh recon-all -base SA14c -tp P10 -tp P11 -tp P12 -all This script was separate from the following step (this was a separate .txt file): recon-all -long P12 SA14c -all -no-isrunning recon-all -long P12 SA14c -brainstem-structures The common error I received from the base template creation: (from the recon-all.error log==uncertain if the recon-all.log would be more illuminating for debugging) $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 user Exp $ /.../.../freesurfer/bin/recon-all PWD /.../.../subjects/SA14c/label CMD mri_label2label --srcsubject fsaverage --srclabel /.../.../subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject SA14c --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface Moreover, with the base template error, it was not possible to go from there to create the individual longitudinal mri output based on the base template I'd be really grateful for help with this debugging! Thank you. Andrew Sunday Willett, M.S. Department of Neurology, Division of Movement Disorders Brigham and Women’s Hospital awillett(a)bwh.harvard.edu<mailto:jkim@bwh.harvard.edu> brighamandwomens.org<http://www.brighamandwomens.org/> [cid:0e0fcfea-f9ea-4981-adad-c366bf0c8f00]

2 1

Recon-all reconstructed image coordinates
by Salar Dini, Elaheh 13 Feb '22

13 Feb '22

External Email - Use Caution Dear Freesurfer developers, In the link below, you see two brains belonging to the same subject: https://secure-web.cisco.com/13BPz3RKb4ouXjNEzLehwPZTK95KDfvYg0N-g887u-w7ft… [https://secure-web.cisco.com/1B08cXHTWamf2XLl-Do2M2Y2jFkmx7hn93F8dK1GfF1Mv6…<https://secure-web.cisco.com/13BPz3RKb4ouXjNEzLehwPZTK95KDfvYg0N-g887u-w7ft…> Screen Shot 2022-01-26 at 1.40.23 PM.png<https://secure-web.cisco.com/13BPz3RKb4ouXjNEzLehwPZTK95KDfvYg0N-g887u-w7ft…> Shared with Dropbox http://secure-web.cisco.com/1qgxtofGxpoR7Sqc5YpeFwa6ndZVhgCVEL8DwdalIfXi80q… while one of them is reconstructed with FS7.2, the other one is reconstructed with a pipeline that uses another code for extracting brain tissue (BET Mask) and then use FS6 for the remaining stages of the reconstruction. While the final result of both constructions matches in most aspects, they don't occupy the same coordinates in space. Is there a way that we can match the coordinates of each voxel for two images? Or in other words make them compatible. The Platform we use is CentOS7 . Thanks and all the best, Ela

2 4

Virtualbox: developer's password
by Francois Leroy 13 Feb '22

13 Feb '22

External Email - Use Caution Hi, I am trying to set-up Freesurfer (fs_ubuntu_18_04_06) from Oracle VM Virtualbox. Could you send me the developer's password useful for login? Thanks for your help Regards Francois

1 0

Re: [Freesurfer] password for FS 7.2.0 Ububntu Virtual Box seetup
by fsbuild 11 Feb '22

11 Feb '22

External Email - Use Caution Hello Malav, Sending to your email shortly. -R. On Feb 11, 2022, at 10:02, Malav Shah <malav.shah(a)bccn-berlin.de> wrote:        External Email - Use Caution        Hi,may I please have the password to FS 7.2.0 Ubuntu Virtual Box setup?Thanks and regards,malavMalav ShahPhD candidate, Michael Brecht Lab,Humboldt University zu Berlin.(+49) 163-216-9391_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

password for FS 7.2.0 Ububntu Virtual Box seetup
by Malav Shah 11 Feb '22

11 Feb '22

External Email - Use Caution Hi, may I please have the password to FS 7.2.0 Ubuntu Virtual Box setup? Thanks and regards, malav Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391

1 0

2 postdoc jobs at Cambridge University
by G. Murray 10 Feb '22

10 Feb '22

External Email - Use Caution 2 jobs, apply by 3rd March 2022 1) deep learning for automated variable sulcal segmentation. 18 month contract (in first instance). Working between Departments of Psychiatry (Suckling, Murray) and Computer Science ('Lio) in Cambridge. Collaboration with JF Mangin in Paris Neurospin. https://secure-web.cisco.com/1RzTC-fQjjzaLeLhUotLnD1_XftnjFj3jGKaC9bep28Wqw… 2) analysis of causes and cognitive and psychiatric consequences of sulcal variability. 36 month contract. Working with above post and further collaborators. https://secure-web.cisco.com/1LTVs5W0EsmnPabG_2tf8Pp46kt5MzX3fg3E2J4FeVJEd0… queries please to gm285(a)cam.ac.uk

1 0

PETSurfer: error: MatrixReadTxT: could not scan value [1][1]
by Jennifer Bramen 10 Feb '22

10 Feb '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to analyze amyloid PET data using PETSurfer. I am trying to do kinetic modeling and I am on the MRTM1 step. I have tried this two ways (one using the wiki instructions and the other using the tutorial ROI-based approach) mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/km.hb.tac.nii.gz --mrtm1 $PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o mrtm1 --no-est-fwhm --nii.gz; done mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/gtm.nii.gz --mrtm1 $PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o $PET_DIR/PREV_019/mrtm1.roi --nii.gz;done Both times I get this error: error: MatrixReadTxT: could not scan value [1][1] I have opened all of the .dat files using my text editor (nano) and they seem ok. I have tried this in other subjects and I get the same error. I searched the list and I cannot find any discussion regarding this error using mri_glmfit and PET data. Anything you can do to help me troubleshoot this error would be greatly appreciated!!! Attached is my time.dat file (I think this is the most likely culprit). Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center

2 3

infant freesurfer with --segfile flag
by Xiaoqian Yan 10 Feb '22

10 Feb '22

External Email - Use Caution Dear Freesurfer expert, I m running infant freesurfer with the --segfile option to do segmentations. The command I use is : infant_recon_all --s bbxx --age xx --segfile <our own segmentaion file> --forceskullstrip The results look great and the wm and pial surface align well with the segmentation file we used. However, I am wondering with this --segfile, which steps the infant_recon_all script is calling compared to those without calling the --segfile option. in addition, with the addition segmentation file provided, we found that the wm surface aligns too well with the 'aseg' file we provided with barely extra smoothing. We are wondering if we could submit our results for you to help us check if that looks reasonable to you. Thank you very much, Xiaoqian

1 0

The fsaverage link points to an older freesurfer version
by Peled, Noam 10 Feb '22

10 Feb '22

Hello, I was running recon-all where SUBJECTS_DIR is /space/megraid/clinical/MEG-MRI/seder/freesurfer, where we store our patient's Freesurfer reconstructions. I received the following error: ERROR: Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an older freesurfer version Indeed, the fsaverage link points to version 6, where we are using 7.1.1 I think it makes sense to change it, but I don't have the permission to do that ( the owner is zkaufman, and the group is fsbuild) Thanks, Noam

1 0

FREESURFER Using Freesurfer files within MATLAB
by Alison McDonnell 10 Feb '22

10 Feb '22

External Email - Use Caution Hi all, I am trying to use my Freesurfer files that were created during recon all in a MATLAB code. Do I need to add something at the start to do so or open MATLAB through the terminal to get these to work? At the moment it is giving an error saying "unrecognized function or variable" for fs_read_surf. Any help would be appreciated. Thanks, Ali

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