Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

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

recon-all
by jiahui 29 Apr '20

29 Apr '20

2 1

mri_label2vol
by Mason Wells 29 Apr '20

29 Apr '20

External Email - Use Caution Hi Experts, I want to take an ROI label that I have drawn on the surface and transform this into the volume. I have drawn the label in the T1 anatomical space and I want to keep the label in this space during the conversion. I am currently using this command based off previous forum posts. mri_label2vol --subject S1 --label S1/prf/mid_contra.label --temp S1/mri/orig.mgz --proj frac 0 1 .1 --fillthresh .3 --hemi lh --o S1/prf/contra.nii.gz –identity Can someone let me know if I am on the right track as when I view this volume in FSLeyes, It doesn’t quite look right. If not, any advice would be greatly appreciated. Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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