Freesurfer March 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
153 discussions

wm.mgz and wmparc.mgz
by Xiaoying Tang 15 Mar '10

15 Mar '10

Hi all, After autorecon3, there are two files named wm.mgz and wmparc.mgz. What's the difference between this two? If I just want the white matter, should I use wm.mgz or wmparc.mgz? The corresponding grey matter is aparc+aseg.mgz. Looking forward to your early reply. Best, Xiaoying

3 2

Pial surface- clarification
by Rajagopalan, Venkateswaran 15 Mar '10

15 Mar '10

Hi All, I am working in ALS dementia patients where there is ventricle enlargement and more CSF filling when compared with controls. Since i am new to freesurfer and my knowledge of anatomy is limited i would like to clarify the following. Pial surface in right and left cerebral cortex looks suspicious to me, the brain extraction step left out some non brain regions, i tried to edit them but since some of the non brain regions are close to brain regions i didn't do too much editing for the fear of removing brain regions. I have attached a screen shot image in one of our subjects, kindly tell me whether the pial surface looks ok if not any suggestions to correct this problem. Thanks in advance venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

2 2

rois based on mni coordinates
by Sharmili 57 14 Mar '10

14 Mar '10

Dear Freesurfer experts, i am trying to construct a roi based on some mni coordinates. I checked the coordinate in tkmedit, saved the point and opened it in tksurfer and transformed the selected vertices into labels. But the coordinates change as soon as I open the point in tksurfer. Is there a function like select_talairach_point for mni coordinates? Thanks a lot for your help! Sharmili _________________________________________________________________ http://redirect.gimas.net/?n=M1003xHM5Adressen2 Ein Postfach für Alles – bei Hotmail 5 E-Mail-Adressen online verwalten!

1 0

ERROR: comparison in expression (FS with SGE)
by Xue, Feng 13 Mar '10

13 Mar '10

Dear Bruce & FS experts, Please forgive my re-post, for I havn't got any response from last post. I do appreciate if anyone could give me a hint or suggestion. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ We are running freesurfer with Sun GridEngine. Currently, we repeatedly got this error in SGE's job error log file on some data when doing recon_all: $ cat recon_xf.e437 (standard_in) 2: Error: comparison in expression $ cat recon_xf.e431 (standard_in) 2: comparison in expression I also checked the recon-all-status.log file, but not error was found. Has anyone met this problem? Is it critical? Thanks in advance. -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org

2 1

Extracting ROIs from aparc.a2009s+aseg.mgz
by liang wang 12 Mar '10

12 Mar '10

Hi FS experts, Does anyone know how to extract these ROIs (including all gyral and sulci) from the image <aparc.a2009s+aseg.mgz>. I just want to create a mask image based on this image by using 1, 2, .. to code different brain areas. Thanks for your solutions. Also, I can not display the image using the following command: tkmedit subjid orig -aux brain -aparc.a2009s+aseg.mgz, but can correctly display <aparc+aseg.mgz>. Any advise would be appreciated. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

2 4

MNI-space label to dicom-space?
by Jesse Friedman 12 Mar '10

12 Mar '10

Hi, I'd like to convert a label from fsaverage/MNI-space to the space of a subject's unpacked, unreconstructed, dicom-format scan. Will this be possible? Thank you, Jesse -- Jesse Friedman Martinos Center for Biomedical Imaging, Manoach Lab Massachusetts General Hospital 149 13th Street #1111 Charlestown, MA 02129 Phone: (617) 726-0307 Fax: (617) 726-4078 jessef(a)nmr.mgh.harvard.edu

1 0

freesurfer and DTI
by Dana W. Moore 12 Mar '10

12 Mar '10

Hello everyone, I have a colleague (cc'd) who is interested in using FreeSurfer's segmentation with DTI results he obtained with TBSS. I am not sure how he should go about this. Any advice is appreciated. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

2 1

optseq installation
by Florence POMARES 12 Mar '10

12 Mar '10

Dear Optseq Developpers, Few years ago we used to design our paradigm with optseq. We would like to use it again but we can't install it. We went on the web site : http://surfer.nmr.mgh.harvard.edu/optseq/ we download the linux version 2 we upload it to the our old linux server with matlab optseq and optseq2 aren't recognize as command. we also tried to install the cywin version on a PCwindows with cygwin and matlab. but when we execute the optseq2.exe it says that it doesn't find the input point of _isnand in the library of the dynmic links cywin1.ddl we don't know what to do. would you please help us ? thank you Isabelle Faillenot Ingénieur hospitalier service de neurologie - CM2R hôpital Nord 42055 Saint-Etienne cédex 2

2 1

problem on recon-all
by Xiaoying Tang 12 Mar '10

12 Mar '10

Hi all, When we do recon-all, we usually do autorecon1, autorecon2, and autorecon3 in sequence. But now suppose I have already have a very good skull-stripped subject. I mean I don't need to do skull-stripping with freesurfer. But I want to get greymatter and white matter, which are generated in autorecon2 and autorecon3. Is there any way to do this? Looking forward to your early reply. Best, Xiaoying

2 2

Performance on brains with tumors
by Chris Filo Gorgolewski 12 Mar '10

12 Mar '10

Hi, how does freesurfer perform on brains with tumor? Are the any specyfic options that could improve the results (like masking for example)? Cheers, Chris

3 2

← Newer
1
...
7
8
9
10
11
12
13
...
16
Older →

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 2010