Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Ubuntu VM password
by Alex Mihai 01 May '20

01 May '20

External Email - Use Caution Hi guys! I have followed the virtual machine setup for virtual box freesurfer installation.but it ask me the password for the developer account. Which is the password? Cheers, Alex

2 1

trac-all -bedp error
by Zeng, Qi 30 Apr '20

30 Apr '20

External Email - Use Caution Hi, I run trac-all, the log file has the following endings. "Queuing post processing stage" or "Queuing post processing stage 59 slices processed All slices processed /hpc/packages/minerva-common/freesurfer/6.0.0/freesurfer/bin/bedpostx_mgh: line 345: kill: (100952) - No such process". However, all outputs described in FSL BedpostX are generated dmri/FA, MD, V1, V2, V3 dmri.bedpostX/merged,mean,dyads, nodif_brain_mask Should I consider them as completed and move forward with -path? Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

2 2

Re: [Freesurfer] FreeSurfer 7 stable
by fsbuild 30 Apr '20

30 Apr '20

External Email - Use Caution Hello Mina, On the setup page under the CentOS7 and 8 header, https://surfer.nmr.mgh.harvard.edu/fswiki//FS7_linux, it does mention you can use the same archive and rpm installer for both CentOS7 and CentOS8.  Or the CentOS7 binaries should be backwards compatible on CentOS8.  We should eventually have a CentOS8 installer from native builds on CentOS8. To make that more clear, I changed the chart for downloads on the page, https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads, so say “use the CentOS7” archive or RPM.  Cuda is no longer officially supported as it is a moving target w.r.t NVIDIA hardware and drivers.  Maybe some other folks on the list have suggestions for GPU's.   I know Apple no longer supports NVIDIA hardware. - R. On Apr 30, 2020, at 19:44, Mina Rizkallah <dr.minafakhry(a)live.com> wrote:        External Email - Use Caution        Greetings FreeSurfer team,I have some questions regarding the latest stable version of freesurfer;1- I am currently using Centos 8, and the Freesurfer download link for this version says centos 7 not 8.. is it compatible with centos 8?2- Is it true that CUDA is no longer available for freesurfer? is there any other option for GPU acceleration? as it was crucial for recon-all speed (got 2.7 hours/subject instead of 6 hours on version 6).best regardsMina_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

longitudinal dmrirc script error with the baselist
by Zeng, Qi 30 Apr '20

30 Apr '20

External Email - Use Caution Hi, I have my trac-all up and running with no error with individual subjects when I set the subject directory to individual subjects. as follow: set SUBJECTS_DIR=/*/subjects/SUBJ1 set subjlist = (SUBJ1_ses-1 SUBJ1_ses-2) set baselist = (SUBJ1_base SUBJ1_base) However, when I put subjects together and set the directory to multiple subjects as follow: set SUBJECTS_DIR=/*/subjects set subjlist = (SUBJ1/SUBJ1_ses-1 \ SUBJ1/SUBJ1_ses-2 \ SUBJ2/SUBJ2_ses-1 \ SUBJ2/SUBJ2_ses-2 \ etc. ) set baselist = (SUBJ1/SUBJ1_base \ SUBJ1/SUBJ1_base \ SUBJ2/SUBJ2_base \ SUBJ2/SUBJ2_base \ etc.) It has a problem finding the baselist file: "cannot find /*/subjects/SUBJ1/SUBJ1_ses-1.long.SUBJ1/SUBJ1_base". Should I copy SUJB1_base under the SUBJ1.long.SUBJ1 and run it again? Why is it not happening with the subject individual? Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

2 3

FreeSurfer 7 stable
by Mina Rizkallah 30 Apr '20

30 Apr '20

External Email - Use Caution Greetings FreeSurfer team, I have some questions regarding the latest stable version of freesurfer; 1- I am currently using Centos 8, and the Freesurfer download link for this version says centos 7 not 8.. is it compatible with centos 8? 2- Is it true that CUDA is no longer available for freesurfer? is there any other option for GPU acceleration? as it was crucial for recon-all speed (got 2.7 hours/subject instead of 6 hours on version 6). best regards Mina

1 0

FreeSurfer version 7.0.0 is now available
by Douglas N. Greve 30 Apr '20

30 Apr '20

We are pleased to announce the release of FreeSurfer version 7. You can get the new software from here https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall You can find the release notes here https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes Let us know how it goes best doug and the FreeSurfer development team

1 0

bbregister & mri_convert
by Octavian Lie 30 Apr '20

30 Apr '20

External Email - Use Caution Dear All, I have seen bbregister command lines using --o option to get the final output (say a .nii vol), and others where bbregister is used to get an lta transform, which is used in a follow-up step (mri_convert with -ns 1 (no scale), and -rl orig.mgz (reslice-like) Are these options equivalent? meaning when using bbregister with '--o x.nii' option, is the output volume x.nii resliced to orig.mgz, and without rescale? Thanks, Octavian

2 2

recon-all
by jiahui 30 Apr '20

30 Apr '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute gray matter volume, but for some of my subjects I get the following error when I run the recon-all -all command: ERROR: inflating to sphere (rms error < 2.00) final distance error I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: ubuntu 16.04.6 LTS 3) recon-all.log and figure2020042908160: see attached

2 1

Quick question on tkregister
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 29 Apr '20

29 Apr '20

?Hi all, I'm a little confused about what the most latest GUI software to fix the talairach is at the moment. This page refers to: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview? but the software, tkregister2 seems to be unavailable. Has it been deprecated by tkregister2_cmdl or tkregisterfv? If so what is the command to open up the GUI with FS6? Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

3 4

Questions about pial_lgi
by 肖伏龙 29 Apr '20

29 Apr '20

External Email - Use Caution hello everyone I have a question about statistics on LGI. for the LGI data, named as lh.pial_lgi, I used mris_preproc as following: mris_preproc --fsgd fsgd.fsgd --cache-in pial_lgi --target fsaverage --hemi lh --out lh.pial_lgi but freesurfer said ERROR: format for lh.pial_lgi not recognized so is there any method to solve this problem? Thank you

3 3

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