Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

autoreco3 error
by LAOUCHEDI MAKHLOUF 03 Jun '13

03 Jun '13

Hi i run recon-all -autorecon3 on a normal subject and after a while, it exited with errors, looking in the SUBJECTS_DIR/subj/scripts/error.log and recon-all.error and recon-all.log i found the following messages : error.log : mrisReadTriangleFile(../surf/rh.smoothwm): surface doesn't match ../surf/rh.inflated mrisReadTriangleFile failed. MRISreadOriginalProperties: could not read surface file smoothwm recon-all.error : . . . PWD /home_cluster/mlaouche/freesurf_makh/ctr5/scripts CMD mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere recon-all.log : mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... mrisReadTriangleFile(../surf/rh.smoothwm): surface doesn't match ../surf/rh.inflated No such file or directory mrisReadTriangleFile failed. No such file or directory MRISreadOriginalProperties: could not read surface file smoothwm No such file or directory Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ctr5 exited with ERRORS at Mon Jun 3 11:38:58 CEST 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting thank you for your help

2 1

Volume acquisition
by elisa veronese 03 Jun '13

03 Jun '13

Hi, I am a beginner in the use of Freesurfer. I was wondering if the T1w volume used as input for the recon-all has to be acquired in axial direction or not. In other words, is there a recommended acquisition direction? Thank you, Elisa -- Elisa Veronese - PhD http://www.dei.unipd.it/~verones1/

2 1

cortical thickness
by 三足乌 03 Jun '13

03 Jun '13

Hi expert, If I want to get the cortical thickness,what will I do in the freesurfer? All suggestions welcome. Thanks in advance, Lucy

2 1

bert recon-all errors, CUDA
by Graham Wideman 03 Jun '13

03 Jun '13

1 0

cvs error
by Fernando Valle-Inclán 03 Jun '13

03 Jun '13

Hi everyone, I´m trying to do cvs registration using freesurfer 5.3 and I get this message: "The following files are missing: /Applications/freesurfer/bin/mri_cvs_register.settings.txt You need to find these files or run reconall on the data in order to run mri_cvs_register" Any idea would be wellcome Thanks Fernando

1 0

Postdoc positions available at the Netherlands Institute for Neuroscience in Amsterdam
by Diederick Stoffers 03 Jun '13

03 Jun '13

Dear all, Please find attached a description of postdoc positions available at the Netherlands Institute for Neuroscience in Amsterdam, which I am posting on behalf of my group leader Eus van Someren (cc). Relevant keywords for these positions are sleep, emotion, arousal, high-density EEG, fMRI, TMS, insomnia, internet assessment, database, latent class and latent trait analysis. Cheers, Diederick NB Apologies if you receive this message twice, the initial message was rejected by some servers because it exceeded maximum message size.

1 0

Problem with recon-all - nu_currect
by Andrea Tateo 02 Jun '13

02 Jun '13

Dear FS experts, I have a problem with the command "recon-all". In many cases when I use it on the same brain's MRI, on the CLUSTER COMPUTING INFRASTRUCTURE, about 40% of my jobs finish without erros while the other are killed at the command "nu_currect", as you can see from the file.log in attachment. Do you have any suggestions? Thanks a lot for your help. Best regardes, Andrea

1 0

recon-all error
by 小麦 01 Jun '13

01 Jun '13

Hi expert, After I had finished the command recon-all -i image -s zxm -autorecon1 without any error,I executed the command recon-all -s zxm -autorecon2,and I met errors,details are as follows. Build stamp:freesurfer-Linux-centos4-stable-pub-v5.1.0 Debain version:5.0 Kernel info:Linux 2.6.28-11-generic i686 the command-line executed:recon-all -s zxm -autorecon2 the error message generated:the first erroris is mri-ca-register with non-zero status 252,but contionuing despite the error the sencond error is cannot find or read transforms/talairach.m3z I want to konw the reasons. All suggestions welcome. Thanks in advance, Lily

2 1

REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2
by Garikoitz Lerma-Usabiaga 01 Jun '13

01 Jun '13

Hi, Has anybody got problems using FS with NFS v4? We cannot write subjects if the SUBJECTS_DIR is in a NFS v4 system. Many thanks, Gari ---------- Forwarded message ---------- From: Garikoitz Lerma-Usabiaga <garikoitz(a)gmail.com> Date: Tue, May 7, 2013 at 5:25 PM Subject: NFS v4 on CentOS 5.4 or Red Hat 6.2 To: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Hi FS experts, we have changed our file systems to NFS v4 and we found that FS cannot write to it (I mean, FS installed in an app server and subjects in the file system is not working). Last new I have is that FS in CentOS could read but not write and in Red Hat could not write or read. Is it a known problem? Is it something going on with FS or the problem is in our end? (the rest of the programs are working fine: FSL, Matlab...) Many thanks, Gari

4 12

CVS crashing consistently: update
by Graham Wideman 31 May '13

31 May '13

Hi MGH folks, Update to previous report: Review: Both of my attempts from scratch to CVS the 5.3.0 source failed after about 760 files, directory trctrain. CVS quit with fatal signal 9 error. Previously when I tried to restart either of these, CVS would quickly run through all the up-to-date directories, then hang at trctrain, with no terminal, disk or network activity (as judged by router lights). I have since let it sit there for probably 20 minutes, and suddenly the process came to life... downloading trctraindata.tar.gz (over 500 Meg). So, I don't know if or why that large file was resulting in signal 9 error, but progress is now unjammed. -- Graham

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