Freesurfer

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30132 discussions

Defacing with mri_deface
by slehar＠nmr.mgh.harvard.edu 03 Jun '13

03 Jun '13

The script mri_deface which is called by recon-all with the -deface flag, requires the existence of two files /usr/local/freesurfer/stable5/average/face.gca /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca The former exists where it should, the latter does not exist at that location, although it can be downloaded from http://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads and gunzipped. When I copy it into a directory and call mri_deface directly, it works OK because it can find that image locally. But when I call recon-all with the -deface flag, it looks for the file where it does not exist, i.e. /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca Could someone with the appropriate permissions please copy that file to where recon-all expects to find it? Second question: If I call recon-all with the -deface flag, does it deface ALL the images in my SUBJECTS_DIR/$subjid/mri directory, or does it only deface a copy of orig.mgz to orig_defaced.mgz?

2 3

use of anot_2_label
by LAOUCHEDI MAKHLOUF 03 Jun '13

03 Jun '13

Hi i used mri_annotation2label to extract the cortical labels. for this command we must specify which hemisphere (--hemi ?h) and i want to extract the brainstem which is not a lateralized structure, is there any command like mri_annotation2label to extract the brainstem ? thanks

2 1

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

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