Freesurfer March 2011

freesurfer@nmr.mgh.harvard.edu

111 participants
170 discussions

FreeSurfer 5.1
by Alan Francis 09 Mar '11

09 Mar '11

Hi Bruce, Nick & Doug: Any chance of FS 5.1 coming out in the near future? We have 2 longitudinal data sets that we are holding back till we have this installed. Thanks so much, Alan

2 1

open .gca file
by Tetiana Dadakova 09 Mar '11

09 Mar '11

Dear FreeSurfer list, I try to open RB_all_2008-03-26.gca by typing mri_convert RB_all_2008-03-26.gca -nth 0 means.mgz and get an error: mri_convert RB_all_2008-03-26.gca -nth 0 means.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from RB_all_2008-03-26.gca... reading frame 0 of gca TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to means.mgz... mghWrite(means.mgz, -1): could not open file ERROR: failure writing means.mgz Could you please tell me what can be wrong? Thank you, Tanja.

2 1

Fixated brain
by Auer, Tibor MD. Ph.D. 09 Mar '11

09 Mar '11

Dear Users, Is there a way to process fixated brain (after autopsy) with Freesurfer? I have read somewhere that I should just "invert" the image, but what does it mean? And would it not increase the noise and the signal from the CSF? Of course, the brain is without any skull, pia and dura mater. Does it cause no problem for Freesurfer? Thanks, Auer, Tibor M.D. Ph.D. Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Germany Phone/Work: +49-(0)551-201-1725 Mobile: +49-(0)176-8012-7921 E-Mail: tauer(a)gwdg.de <mailto:tibor.auer@gmail.com>

1 0

Miao Wen wants to stay in touch on LinkedIn
by Miao Wen via LinkedIn 09 Mar '11

09 Mar '11

LinkedIn ------------Miao Wen souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, I'd like to add you to my professional network on LinkedIn. - Miao Wen Accepter l'invitation de Miao Wen http://www.linkedin.com/e/-qq80um-gl1us5y3-j/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59… Voir l'invitation de Miao Wen http://www.linkedin.com/e/-qq80um-gl1us5y3-j/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59… ------------------------------------------ SAVEZ-VOUS que votre profil LinkedIn vous permet de contrôler votre image professionnelle sur le Web ? Si vous le rendez "public", votre profil LinkedIn apparaîtra quand un internaute effectuera une recherche en ligne sur votre nom. Soignez votre image sur le Web ! http://www.linkedin.com/e/-qq80um-gl1us5y3-j/ewp/inv-22/ -- (c) 2011, LinkedIn Corporation

1 0

Newbie - problems compiling project tree
by Shay Ohayon 08 Mar '11

08 Mar '11

Hi All, I am having some problems compiling freesurfer . I checked out the recent development version from the CVS, ran "setup_configure" successfully, but upon "./configure", I end up with the following annoying message: checking for nccreate in -lnetcdf... no configure: error: FATAL: netcdf lib not found. Set LDFLAGS or --with-mni-dir. I attempted to install the netcdf-bin and libnetcdf6 packages using Synaptic, but this did not seem to help. How do I continue from here? -- Shay

2 2

Pial view
by Allie Rosen 08 Mar '11

08 Mar '11

Hi Everyone, I am hoping to visualize the insula using the pial view in TkSurfer. Is there a way to make the surfaces translucent, or to crop away specific areas? I would like to use the pial view instead of inflated views to do this. Thanks, Allie Rosen, MSc Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto

2 1

Intensity Problem
by Matt Russell 08 Mar '11

08 Mar '11

Dear FreeSurfer Experts, I'm currently working with a data set that seems to have a systematic problem with intensity. I attached an image of a brain with this problem for your reference. As you can see, the unprocessed MRI file has an intensity problem in the temporal lobe, almost like a flashlight is lighting it up. When FreeSurfer processes this part of the brain it fails to detect it. My question is a) is this data still usable? We aren't actually looking for any effects in this area of the brain, but are worried that it is a bigger symptom of problematic data and b) if this data is still usable, is there anything we can do to work around it? Thanks, Matthew Russell

3 5

CUDA comparable to non-CUDA?
by Marcus N Schmidt 08 Mar '11

08 Mar '11

Hi FreeSurfer Experts, Just a quick question: Generally speaking, assuming everything else remains the same, are subjects run through a CUDA-enabled recon-all comparable to subjects run through recon-all without CUDA? Thanks, Marcus Marcus N Schmidt Department of Child & Adolescent Psychiatry Erasmus MC Rotterdam, The Netherlands

3 3

Re: [Freesurfer] Path Setup of FREESURFER_HOME
by Andrew Jahn 08 Mar '11

08 Mar '11

Hello, I just downloaded and installed Freesurfer onto a new computer, and after going through all the steps outlined on the download and installation page, I get the following error when trying to run recon-all: sudo recon-all -s bert -all FREESURFER_HOME: Undefined variable. However, I have set an absolute path to FREESURFER_HOME: -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni Any ideas on what is going on? I would appreciate any feedback. Thanks! -Andrew

1 0

volumetry longitudinal comparison...
by Gonzalo Rojas Costa 07 Mar '11

07 Mar '11

Hi: I want to do a longitudinal comparison of the aseg volumetry of the same patient with two MRI in different dates... How can I do it ?... any freesurfer tool ?... qdec ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

2 3

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 March 2011