Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30090 discussions

Cortical thickness
by Joshua deSouza 03 Jun '13

03 Jun '13

Hello everyone, Please pardon my rather simple question I have done a GLM fit anlysis and have obtained a file sig.mgh alonf with a few others after the analysis.As I know, I do not have to create ROIs in order to do this. I also understand that doing a multiple comparison analysis just compares the regions of importance and evaluates them giving the most resilient cluster depending on the threshold. So, this does not give a thickness estimate. I would like to know how do I get the cortical thickness values from the results? If so, can I do it after glmfit? And thanks Doug for your help in the other questions that I had prior to this! Thank you

3 7

(no subject)
by Shani Ben Amitay 03 Jun '13

03 Jun '13

Hello all I have created white matter surface of a non primate brain and I'm trying to use mris_make_surfaces to position the pial surface. The problem is that the resulted pial surface is miss-positioned-the 'growing' stops very close to the white surface (no gradient visible where it stops) Any idea what could be the reasons ? Thanks, Shani

2 1

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

03 Jun '13

2 1

mris_resample: Command not found.
by Barron, Daniel S 03 Jun '13

03 Jun '13

Hello, I am trying to perform an inter-subject registration using mri_cvs_register on version 5.3. When I ran mri_cvs_check, my feedback was I needed to find "mri_cvs_register.settings.txt" but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.ht… mri_cvs_register kicks off well, but eventually it ends with: "mris_resample: Command not found." I go into my $FREESURFER_HOME/bin directory and note that mris_resample is truly not there. Did I not install 5.3 properly? I have attached a log file in case this helps. Cheers, Daniel

4 7

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.

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