Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

save custom made path on surface as label
by Erhan Genc 05 Mar '12

05 Mar '12

Dear freesurfer experts, I draw a path with the tksurfer tools on a surface, but was not able to save this path as a label. During the custom fill step it marked the whole surface and not just the path. I think it is because the path is not closed. Is there still a way to get a path as a label file? cheers, erhan -- Dipl. Psych. Erhan Genc Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt am Main -GERMANY- phone: +49 (69) 96769-471 fax: +49 (69) 96769-327 e-mail: genc(a)mpih-frankfurt.mpg.de http://www.brain.mpg.de/research/singer-emeritus-department/people/erhan-ge…

1 0

Changing the settings in TkMedit .tcl file
by Stephen Politzer-Ahles 03 Mar '12

03 Mar '12

Hello, I am trying to change some default settings in TkMedit by specifying my own .tcl file (using the *-tcl* flag when I call *tkmedit*), and I'm finding that some of the changes work and some do not. Here is my tcl: SetBrushShape 10 0 1 > SetTool 2 > SetDisplayConfig 2 2 0 > I got those settings from surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditReference/TkMeditScri…. I saved that in a file called tkmedit_defaults.tcl, and when I open TkMedit I call tkmedit <subject> T1.mgz -tcl $FREESURFER_HOME/tktools/tkmedit_defaults.tcl . When TkMedit opens, the tool has been set to Edit Voxels like I hoped, and the brush has been set to Circle with a radius 10 like I hoped. But it's not set to 3d (which I thought the "1" in SetBrushShape 10 0 1 would do), nor is it set to a 2x2 display from SetDisplayConfig. Does anyone have any guesses what might be causing those commands not to work? The version of freesurfer I'm using is freesurfer-x86_65-redhat-linux-gnu-stable5-20110522, which I believe is more or less the newest version. Thank you, Steve Politzer-Ahles

1 0

improve aparc+aseg result
by Ping-Hong Yeh 03 Mar '12

03 Mar '12

Hi, Our data do no get good parcellation and segmenation, mainly in the subsulcal and subcortical regions (see the attached examples), which are likely due to imhomogeneity bias and/or brain lesion. Adding control points and WM matter edits do not seem to help. Any suggestion in improving? Thank you, Ping

2 1

mri_glmfit problem with y option
by Charlotte Bernard 02 Mar '12

02 Mar '12

Dear Freesurfer users, I have tried to run mri-glmfit but I have obtained the error message: ERROR: Option --y unknown I don't understand why! I have run that command line: mri_glmfit \ --y lh.test.thickness.10.mgh \ --fsgd test.fsgd dods\ --C group.diff.mtx \ --surf fsaverage lh \ --cortex \ --glmdir test.glmdir Could somebody help me? Thanks for all, Charlotte

3 2

Postdoc fMRI Reaching and Grasping, Center for Mind/ Brain Sciences, Italy
by angelika lingnau 02 Mar '12

02 Mar '12

*Postdoc fMRI of Reaching and Grasping, Center for Mind/Brain Sciences, University of Trento, Italy* At the Center for Mind/ Brain Sciences (CIMeC), University of Trento, there is soon going to be an opening for a Postdoctoral Fellowship to work with Dr. Angelika Lingnau (http://www.unitn.it/en/cimec/11702/angelika-lingnau) in collaboration with Prof. Raffaella Rumiati, SISSA. In this project, we will use fMRI to study the effects of parietal and premotor lesions on reaching and grasping movements. *Start date:* as soon as possible *Requirements: * PhD in related field Experience with fMRI design and analysis Programming skills (Matlab or C) The Center offers an international and vibrant research setting with access to state-of-the-art neuroimaging methodologies, including a research-only 4T MRI scanner, MEG, EEG and TMS, as well as behavioral, eye tracking and motion tracking laboratories. The University of Trento is ranked first among research universities in Italy. English is the official language of the CIMeC, where a large proportion of the faculty, post-docs and students come from a wide range of countries outside of Italy. For informal inquiries, please contact Angelika Lingnau ( angelika.lingnau(a)gmail.com <angelika.lingnau(a)unitn.it>).

1 0

Data check
by Charlotte Bernard 02 Mar '12

02 Mar '12

Dear Freesurfer users, I would like to know what is the procedure to check the quality of the Freesurfer process on my subjects. I have more than 500 subjects. 1/ Have I to check each segmented region on by one for each subject? 2/ How can we check the quality of the surf process? Thanks a lot for your help, Charlotte

1 0

Recommended reconstruction wiki
by Martijn Steenwijk 02 Mar '12

02 Mar '12

Dear all, On http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction it is indicated that -autorecon-cp should be added if control points are added. Shouldn't this be -autorecon2-cp? Furthermore, suppose control points are added and -autorecon2-cp has been runned. If I then correct the skull strip (as indicated in the wiki) and want to rerun, do I have to call -autorecon2-cp then, or can I just run -autorecon2 -autorecon3? Best, Martijn

3 8

Tracula preproc failure
by Martijn Steenwijk 01 Mar '12

01 Mar '12

Dear all, I'm running Tracula on a brain with some pathology. During the preproc phase it fails with the following error: INFO: Rejected 843 streamlines for straying off mask INFO: Rejected 0 streamlines for reversing direction INFO: Rejected 10 streamlines as length outliers INFO: Have 2748 total streamlines (min/mean/max length: 38/70/105) Processing pathway 3 of 18... Matching streamline ends INFO: Have 0 non-truncated streamlines (min/mean/max length: 0/0/0) INFO: Center of mass of start points: (nan+/-nan, nan+/-nan, nan+/-nan) INFO: Center of mass of midpoints: (nan+/-nan, nan+/-nan, nan+/-nan) INFO: Center of mass of end points: (nan+/-nan, nan+/-nan, nan+/-nan) Segmentation fault (core dumped) Linux lnx-rad-03 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST 2008 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Feb 27 19:41:00 CET 2012 I understand that no streamlines are available for initialization. Is that correct? Best, Martijn

3 3

Probabilistic white matter mask
by Palzes, Vanessa 01 Mar '12

01 Mar '12

I found a couple older threads about creating a probabilistic mask in Freesurfer: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11790.html https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-July/014953. html I have modified mri_ca_label with the flag -write-probs and instead of norm.mgz I use aseg.mgz: mri_ca_label -align -nobigventricles -write-probs aseg.mgz transforms/talairach.m3z /Applications/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz Freesurfer then tells me: "writing label probabilities to aseg.mgz" - so I assume that is a success. Now in order to extract a white matter mask, I have tried both mri_extract_label and mri_binarize (although the point of this one is to binarize) to extract these probability values of the white matter areas from aseg.mgz. Unfortunately, I am not getting any probability values in the mask, neither in the form of 0-255 nor 0-1. I've tried searching for another command I can use to create masks, such as mri_wmfilter but I think that one is outdated since it looks to a specific directory called "brain" within the subject folder. Is there another command I can use to extract masks with probability values? Or do I need to run the remaining pipeline of commands after mri_ca_label in order to achieve this? Your help is greatly appreciated. Thanks, Vanessa Palzes Staff Research Associate Brain Imaging & EEG Lab San Francisco VA Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155 -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Thursday, March 01, 2012 9:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 97, Issue 1 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."

2 7

Qdec Error: MatrixMultiply: ml is null!
by Laura Tully 01 Mar '12

01 Mar '12

Hi, I am trying to run a between group analysis in QDEC whilst controlling for intrancranial volume. The design has one dichotomous variable (group2, group2), one continuous (performance on behavioral task), and one nuisance variable (intracranial volume). each time I run it qec crashes with the following error: MatrixMultiply: ml null! What does this error mean and how can I fix it? What is odd is that this error does not seem to be consistently reproducible - after successfully running the analyses without controlling for ICV, I was then able to run it with ICV as a nuisance factor. Thank you! Laura. -- Laura Tully Social Neuroscience & Psychopathology Harvard University 806 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully(a)fas.harvard.edu

3 9

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