Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Tksurfer overlay custom color look up table
by Julien Dubois 13 Oct '09

13 Oct '09

Hello everyone is there a way to display an overlay in tksurfer with a clut other than the three available from the gui? Thanks a lot in advance. - Julien

2 1

SUBJECTS_DIR problem when trying to goregister functional and structural data
by Natalia Zaretskaya 13 Oct '09

13 Oct '09

Hi all, I am doing retinotopy with freesurfer and fsfast on Mac OSX. Made the data directory structure as required. When I try to coregister anatomical and structural data with tkregister-sess -sf sessid -regheader I get the following message: -------------------------------------------------------------- tkregister-sess logfile is /applications/freesurfer/retinotopy/log/tkregister-sess.log -------------------------------------------------------------- Session: /applications/freesurfer/retinotopy/CA ---------------- Tue Oct 13 13:47:18 CEST 2009 is not in SUBJECTS_DIR SUBJECTS_DIR is /Applications/freesurfer//subjects I would appreciate any help/hints on what might have gone wrong.

2 1

Re: [Freesurfer] skull stripped image with the original resolution
by Jose Luis Cantero Lorente 13 Oct '09

13 Oct '09

2 1

CentOS5.3 and freesurfer
by tulu 13 Oct '09

13 Oct '09

Dear FS Experts, Is it compatible to use CentOS 5.3 for install freesurfer ? both tksurfer and tkmedit, freeview can run successfully ? Any suggestion is helpful Thanks in advance Jung lung hsu

2 1

surf2surf for annots
by Alex Fornito 13 Oct '09

13 Oct '09

Hi all, I have a custom annot in fsaverage space that I would like to map to the surface of each of my subjects. I have 2 questions about how mri_surf2surf does this: 1 - Does it use the surface-based registration performed in autorecon2, or is it a volume-based registration? 2 - If it is a volume-based registration, is there any way to use the surface-based registration for this mapping, as I presume it will be more accurate? Thanks for your help, Alex

2 1

Poor grey and white matter segmentation
by Angel Wong 13 Oct '09

13 Oct '09

Dear all Actually I would like to perform automated reconstruction for my T1 image and then obtain anatomical labels after cortical parcellation. I have done fully automated reconstruction using recon-all. But for my case, the white and grey matter segmentation appears to be weird. The green line seems laying on the pial surface rather than on the white surface, and the red line seems including some non-brain structures (including small portion of CSF and skull). Thus, the resultant cortical thickness appears to be very thin after the segmentation. I just doubt if anything was going wrong during the procedure. Or need any preprocessing to enhance the segmentation quality before performing the reconstruction? If you have had similar situation as mine, please let me know how to tackle the problem. Attached please find the images for better illustration. fs_image_brain.tiff - use brain.mgz as aux volume fs_image_norm.tiff - use norm.mgz as aux volume fs_image_brainmask.tiff - use brainmask.mgz as aux volume and load segmentation file aseg.mgz Thanks Angel

3 13

using mri_convert
by Chaleece Sandberg 12 Oct '09

12 Oct '09

Hello, I am trying to configure freesurfer on our Ubuntu machine so that I can use mri_convert to convert dicom files to nifti files for use in FSL. Our tech guy downloaded and installed it and when I typed mri_convert in the terminal, I got the help information. However, when I tried to actually use the command I got this: *$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I0001.dcm... -------------------------------------------------------------------------- ERROR: FreeSurfer environment FREESURFER_HOME is not defined. If you are outside the NMR-Martinos Center, please set this variable to the location where you installed FreeSurfer. If you are inside the NMR-Martinos Center, please source the standard environment. If you need to install FreeSurfer, go to: http://surfer.nmr.mgh.harvard.edu* So I looked up online how to configure freesurfer, followed the directions and got this: *-------- freesurfer-Linux-centos4-stable-pub-v4.4.0 -------- 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 * So I thought it was done correctly, but when I tried the mri_convert command again, I got the same exact error. I thought I might have been missing the license file, but when I tried to copy the .license text file to the /usr/local/freesurfer directory, I got a message that there was already one there (but I don't see it when I type ls). What am I missing or doing wrong? Thanks, Chaleece -- Chaleece Sandberg, M.A. Graduate Student Speech Language and Hearing Sciences Boston University Sargent College

2 1

N3 -V1.0 option
by McLean John (NHS Greater Glasgow & Clyde) 11 Oct '09

11 Oct '09

Hi, I've been trying to run nu_correct with the -V1.0 and -distance option as follows: nu_correct -V1.0 -distance 50 'myinputfile.mnc' 'myoutputfile.mnc' It seems to run ok, and an output file is created, however, when i look at the corresponding .imp file, it says the Version is 0.9 I've just noticed that the other options in the .imp file, described as the -V1.0 default options in the nu_correct usage page (fwhm, shrink etc), are set to the correct parameters for v1.0, I guess this means that version 1.0 has been run ok then, right? A little reassurance would be great! Many thanks John ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSI recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere For more information and to find out how you can switch, visit www.connectingforhealth.nhs.uk/nhsmail ********************************************************************************************************************

1 0

RES: reference paper of freesurfer...
by Pedro Paulo de Magalhaes Oliveira Jr 09 Oct '09

09 Oct '09

Yes. There are many papers. Try the section of the wiki: How to cite FreeSurfer. -- Enviado do meu celular Nokia E71 -----Msg original----- De: Gonzalo Rojas Enviado: 09/10/2009 19:07:05 Para: freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] reference paper of freesurfer... Hi: I need to put in a paper the main reference of freesurfer... Which?... I am searching it in the freesurfer wiki, but it appears many papers related to freesurfer... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

reference paper of freesurfer...
by Gonzalo Rojas 09 Oct '09

09 Oct '09

Hi: I need to put in a paper the main reference of freesurfer... Which?... I am searching it in the freesurfer wiki, but it appears many papers related to freesurfer... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

1 0

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