Freesurfer May 2008

freesurfer@nmr.mgh.harvard.edu

63 participants
95 discussions

talairach_avi
by Juranek, Jenifer 22 May '08

22 May '08

Just curious... 1) was talairach_avi (or more specifically, 4dfp suite) introduced with any particular version# of freesurfer? Or has it always been the default? 2) Any comments on differences/similarities with mritotal as called by the -use-mritotal flag within freesurfer? Many Thanks, Jenifer

2 1

Tksurfer vertex array
by Keller, Corey J. 22 May '08

22 May '08

Hi Freesurfers, I am trying to develop an accurate intracranial electrode placement visualization tool with a patient's pre-op MRI and post-op CT. With the pre-op MRI we can do a freesurfer cortical reconstruction and output that surface in talairach space. Has anyone had any luck with co-registering a cortically reconstructed surface with a CT scan with intracranial grid electrode artifacts? Sorry, this is not necessarily a freesurfer question but thought it was a good place to ask. Thanks in advance. Best, Corey -------------------- Corey Keller Epilepsy Unit Clinical Research Coordinator Massachusetts General Hospital Wang 735, 55 Fruit Street Boston, MA 02114 Phone 802.578.6292 Email cjkeller(a)partners.org ckeller(a)nmr.mgh.harvard.edu

1 0

retinatopy question
by Elif SIKOGLU 21 May '08

21 May '08

Hello, I have a basic question regarding retinatopy analysis. In the paradigm files we specify whether the run was mapping eccentricity or polar angle stimulus, and we specify the number of cycles in mkanalysis. Don't we need to be more specific about the stimulus, i.e. how many wedges trace one cycle or the duration of each wedge? Thanks,

4 3

WM parcellation regions
by Marlisa Isom 21 May '08

21 May '08

Hi everyone, Our group is interested to know whether there is a way to view the WM parcellation regions as you would gray matter. My understanding is that the viewer options are for white matter hemisphere totals, as in it's either left or right. Thanks again! Marlisa Marlisa Isom Research Coordinator Head Research Laboratory Washington University in St. Louis (314) 935-8033

2 1

segmentation problem
by Dick, Rachel 21 May '08

21 May '08

Hello, I'm having some issues with the cortex as seen in the attached picture. I know in the more medial regions I can add control points to the white matter to help the pial line extend further out. However, laterally, I'm not sure how to include that cortex that is left out. Any help would be greatly appreciated. Thanks in advance, Rachel

2 1

a problem
by yczhang 21 May '08

21 May '08

Using lgi or thickness,how could I know the anatomical correspondence for a statistical difference area which had been found between patients and controls. I have to report the significant regions ,for example ,postcentral sulcus or posterior cingulate Thanks! yczhang 2008-05-21

2 1

missing libg2c.0.dylib
by Jose Miguel Selman 21 May '08

21 May '08

Hi everyone: I have run freesurfer on Centos for a while now with no problems. I installed the most recent version on a MacBook pro. Tkmedit and Tksurfer work fine, but when attempting the recon-all processing I get an error of a "missing libg2c.0.dylib". The last part of the log follows: --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- dyld: Library not loaded: /usr/local/lib/libg2c.0.dylib Referenced from: /Applications/freesurfer/bin/gauss_4dfp Reason: image not found Trace/BPT trap ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133 ERROR: mpr2mni305 execution aborted ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin jose-miguel-selmans-macbook-pro.local 9.2.2 Darwin Kernel Version 9.2.2: Tue Mar 4 21:17:34 PST 2008; root:xnu-1228.4.31~1/ RELEASE_I386 i386 recon-all exited with ERRORS at Tue May 20 18:46:49 GMT+4 2008 I tried to get information on the list but could not find anything. Thanks Dr. Jose M Selman Confidencialidad: La informacion contenida en este correo y cualquier archivo adjunto es de caracter confidencial. La utilizacion, distribucion, divulgacion o reproduccion esta autorizada exclusivamente para su(s) destinatario(s). Si ha recibido este correo por error, por favor notifiquelo a su remitente y eliminelo completamente de sus recipientes. Clinica Las Condes se lo agradece.(Los acentos han sido suprimidos intencionalmente para no exponer al texto a reemplazos de los caracteres acentuados.) The information contained in this e-mail and any attached files is strictly confidential. Its use, distribution, publication or reproduction is exclusively authorized for its addressee. If you have received it by error, please notify its sender and eliminate it completely from your files. Clinica Las Condes thanks you.

3 4

a problem
by yczhang 20 May '08

20 May '08

Using lgi or thickness,how could I know the anatomical correspondence for a statistical difference area which had been found between patients and controls. Thanks! yczhang 2008-05-21

1 0

Question regarding computing contrasts with mri_glmfit
by Avram Holmes 20 May '08

20 May '08

All, I'm just looking for a little advice on constructing fsgd and .mat files. I would like to compare a healthy control sample with the data from two MDD groups. To do so I made my fsgd file to look like the following: GroupDescriptorFile 1 Title MoneyGame_Subjects Class Control Class MDD Class Anhedonic Input REWARD111 Control Input REWARD201 Anhedonic Input REWARD207 MDD Input REWARD208 Anhedonic Input REWARD211 MDD Input REWARD212 MDD Input REWARD213 Anhedonic Input REWARD215 Anhedonic Input REWARD277 Control Input REWARD278 Control .... This file results in a design matrix with 3 columns. I am interested in conducting the following analyses and I wanted to check to see if I am coding all of the .mat files correctly. Controls vs all Patients (1 -.5 -.5) Anhedonic vs MDD (0 1 -1) Controls vs Anhedonic (1 0 -1) Controls vs MDD (1 -1 0) Thank you in advance for any help you can offer. Avram -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

2 1

Possible to regress whole-brain functional data against continuous variables in the volume?
by Dan Dillon 20 May '08

20 May '08

Hi FreeSurfers. Is it possible to regress functional data against a continuous variable in the volume? I'm analyzing a reward processing study that activates sub-cortical and cortical regions, and I'd like to regress those data against a continuous measure of depressive symptoms administered to each participant. I understand the basic fsgd/mri_glmfit approach from the FS tutorial, but I want to stay in the volume in order to examine sub-cortical structures (e.g., nucleus accumbens). Is this possible? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: dillon(a)wjh.harvard.edu

2 1

← Newer
1
2
3
4
5
6
7
8
9
10
Older →

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer May 2008