Freesurfer July 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
135 discussions

Fwd: Re: question: qdec vs GLM DODS
by Rosa Steimke 10 Jul '09

10 Jul '09

Hi! i have a question regarding the differences between qdec and glm dods. im trying to find out how to analyze my data. I have 1-2 variables of which I want to see the relation to thickness (Autism (discrete) + Empathy (continuous))and maybe 1-2 (gender+IQ) variables that I would want to controle for. Now i cannot understand whether it would be better for me to use the General Linear Model DODS or qdec. What are the differences/advantages. thanks in advance. Rosa Rosa Steimke Student Master of Neuroscience Vrije Universiteit Amsterdam -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01

2 1

4D to 3D
by Mayuresh Korgaonkar 10 Jul '09

10 Jul '09

Dear Freesurfer authors, I have been working with the command line group analysis tutorial from the freesurfer wiki website. Unfortunately I did not "qcached" my data with recon-all. So I ran the "mris_preproc" and "mri_surf2surf" commands from the tutorial (see below) at the end of which I get a single 4D file "lh.gender_age.thickness.10B.mgh" concatenated over all subjects Is there a way to split this file into 3D files so that I have a thickness file for each individual subject? Thanks, Mayuresh mris_preproc --fsgd gender_age.fsgd \ --target fsaverage --hemi lh \ --meas thickness \ --out lh.gender_age.thickness.00.mgh mri_surf2surf --hemi lh \ --s fsaverage \ --sval lh.gender_age.thickness.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.gender_age.thickness.10B.mgh Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com

3 2

v.4.0.5 cross-sectional & v.4.4.0 longitudinal
by Elizabeth Selgrade 10 Jul '09

10 Jul '09

Hello, Can I use v.4.4.0's longitudinal processing stream on scans that I cross-sectionally segmented with v.4.0.5? If so, do I need to rerun any steps of the cross-sectional processing before using these segmentations as inputs in the longitudinal processing? I know a similar question was already posted on the listserve. I apologize for asking again, but I can't find the response. Many thanks! Liz Selgrade --- Elizabeth S. Selgrade Research Health Science Specialist VISN 6 MIRECC Durham, NC

1 0

image matrix
by Feng-Xian 10 Jul '09

10 Jul '09

Hi, I want to check the image matrix after doing autorecon-all. When I look at the text, I see that “Original Data has (1, 1, 1) mm size and (224, 256, 160) voxels. Data is conformed to 1 mm size and 256 voxels for all directions”. This is said that that image matrix is 256 x 256 x 256. Right? And, I want to know how many voxels do an inflated surface have? Where dir and what text do I to get that? And, do FreeSurfer have a text that including the value of cortical thickness? I want to know the information of cortical thickness’s value at all pixels of whole brain for each subject. If yes, what text has the information of the value of cortical thickness and where do I find that text? If no, how can I get the information? Thank you in advance! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

2 5

Surface based volumetry vs Voxel based morphometry
by Pedro Paulo de Magalhães Oliveira Junior 09 Jul '09

09 Jul '09

It's more a methodological question, and I have asked this before, but I think it could be better discussed in the FreeSurfer community. Several times people ask me what's the advantage of Surface based methods like the ones used in FreeSurfer over VBM in estimating volumetric parameters of subcortical structures. The plain question people ask me is: what`s the advantage of FreeSurfer over SPM in terms of volumetric measures. I have some answers for this. I have wrote something about in the FAQ of FreeSurfer but I was wondering if there's some comparative study or some better idea on this. ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business

2 3

pial surface
by Barnali Basu 09 Jul '09

09 Jul '09

Experts, I have successfully run recon-all (all the 3 processes autorecon1,2 and 3) on a subject. When I see the surfaces on tksurfer, I dont get to see the pial surface. I gather I could construct Pial surface by running autorecon2-pial. Would this affect in any way, since I have already finished autorecon3. Do I have to run autorecon3 again ? Any help would be appreciated Thanks Barnali

2 1

FW: difference # vertices in sphere&
by Kirk Gregory R. 09 Jul '09

09 Jul '09

hi q. from a collaborator, someone got a comment for 1 subject the # of vertices of sphere file different from the length of thickness data for the same subject. thanks Greg. -----Original Message----- From: Deepti Pachauri [mailto:deepti.pachauri@gmail.com] Sent: Wed 6/24/2009 1:02 AM To: Kirk Gregory R. Subject: Re: Help Deepti with some questions Dear Greg I have been looking at FreeSurfer data provided by you for 21 subjects(AD/Control). For P1_AD subject I found the # of vertices of sphere file different from the length of thickness data for the same subject. # of vertices for P1.AD subject are 131364 and length of thickness data for the same subject is 131215. However for rest 20 subjects # of vertices and length of thickness data are same. I am using MATLAB to read thickness.asc data and last column is thickness (mm) at given x,y,z. For vertices and faces I am using the standard freesurfer_read_surf.m form http://eeg.sourceforge.net/doc_m2html/bioelectromagnetism/freesurfer_read_s… I am just wondering how to fix this discrepancy of freesurfer output? Also thickness data P10 is missing in asc folder. Sphere and pial files are present in surf folder for P10 subject. Thanks On Tue, Jun 23, 2009 at 3:55 PM, Vikas Singh <vsingh(a)biostat.wisc.edu>wrote: > Hi Greg, > > Deepti, a new CS grad student (copied on this email) is studying the > cortical surface characterization problem, and using the output you > generated. Is is possible that you can answer some of her questions > regarding FreeSurfer? I am copying her on this email. I am out of town > until July 16th, and we wanted to get on top of this over the summers. > Please let us know, possibly with a phone number she can reach you at. > > regards, > > Vikas. > -- Deepti Pachauri

2 1

segmentation
by simon＠cyceron.fr 09 Jul '09

09 Jul '09

Hi. I'm a new user of freesurfer. The default settings of recon-all performed a good white segmentation of my data but I find that grey matter (see attached picture) could be optimized when I look at aseg.mgz results. Indeed the surface cortical grey matter was not extend as expected. What were the different parameters that I can optimize to have a better grey matter segmentation without manual correction? Thank a lot for your answers. Gregory SIMON

2 1

contrast matrix
by Feng-Xian 09 Jul '09

09 Jul '09

Hi, I want to analysis three independence groups. And, I want to display a result of A group > B group > C group with positive(red) and A group < B group < C group with negative(blue). To show that, how do I write the number of columns in the contrast matrix? Thank you in advance! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

2 2

POSTDOC POSITION OPEN
by Juranek, Jenifer 08 Jul '09

08 Jul '09

Subject: POSTDOCTORAL POSITION - structure & function of fronto-cerebellar circuits in neurodevelopmental disorders Applications are invited for an immediate postdoctoral opening in the Department of Psychology at the University of Houston, Houston TX. The position is full-time for 1 year, with the possibility of annual extensions up to 2 years, depending on funding. The current opening entails analysis of already collected MRI datasets from children with and without a neurodevelopmental disorder and relating quantitative MRI findings to neuropsychological assessments. The successful candidate will be responsible for processing and analyzing structural data and writing up the results for publication in peer-reviewed journals. Essential skills include demonstrated knowledge of structural MRI analysis techniques, including Freesurfer and FSL. While this position requires some technical skill with image analysis, it is best suited for someone who is interested in understanding brain-behavior correlates of cognitive function in children with and without a developmental disorder rather than someone with a strict methods development orientation. Applications are welcomed from current Ph.D. students who will have submitted their dissertations in the near future. The position is available for a start date as soon as July 15th 2009. Salary is expected to be $40,000, depending on knowledge and experience, and will come with full health and other benefits at the University of Houston, Houston TX. Non US citizens are welcome to apply. Please send enquiries or applications (which must include a covering letter detailing professional objectives and interests, CV, and the names and email addresses of three references, all together in one pdf file) to Dr. Jack M Fletcher, jmfletch(a)central.uh.edu<mailto:jmfletch@central.uh.edu> , with the subject line "Postdoctoral imaging position". ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ Jenifer Juranek, PhD Assistant Professor Developmental Pediatrics University of Texas Health Science Center at Houston 713.500.3813 (voice) Jenifer.Juranek(a)uth.tmc.edu

1 0

← Newer
1
...
7
8
9
10
11
12
13
14
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 July 2009