Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

segementation
by GaBbo Go. Es. 13 Jan '09

13 Jan '09

hello i'm asking about a the cerebellum segmentation,i'm sending someimages, wich are exacly the same slice, but in two views(coronal and sagital)in those slices y show how looks the cerebellum together with cortex, and how i separated them. Thanks Gabriel. _________________________________________________________________ Chatea sin límites en Messenger con la tarifa plana de Orange http://serviciosmoviles.es.msn.com/messenger/orange.aspx

1 0

Res: [Freesurfer] Segmentation
by Kelly Silva 13 Jan '09

13 Jan '09

Hi, Bruce I´m sending some pictures of aseg.mgz. Is this well done? Is there any objective and specific criteria to separate the cerebelum from the cortex? Is really necessary to do the manual segmentation on that area? Thanks, Kelly ________________________________ De: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Para: Kelly Silva <kcasilva(a)yahoo.com.br> Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Enviadas: Segunda-feira, 12 de Janeiro de 2009 15:40:34 Assunto: Re: [Freesurfer] Segmentation Hi Kelly, did you check the aseg.mgz? Did it separate them properly? cheers, Bruce On Mon, 12 Jan 2009, Kelly Silva wrote: > Hello, > I´m sending an image and I want to know how is the best way to separate cerebelum from the cortex with the preservation of the both structures. > Thanks! > Best regards, > Kelly > > > Veja quais são os assuntos do momento no Yahoo! +Buscados > http://br.maisbuscados.yahoo.com Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

1 0

Cortical thickness in WM disease - experience
by Martin Kavec 13 Jan '09

13 Jan '09

Hi, I have been running quite a few clinical subjects (close to 300) through FS pipeline and comparing cortical thickness from parcellated cortex for each individual subject to its agematched controls. The subject clinical symptoms are not specific, ranging from amnesia, reduced ability to generate words, confusion, ... Every now and that I see that the cortical thickness is suspiciously higher than STD of the controls even if there are no leftovers after brain extraction (I specifically verify it, and if necessary do the corrections). In the vast majority of these cases I also find lower total white matter volume. I am speculating, if possible subcortical WM disease (as detected by reduced total volume of the WM) may come into the play. If subcortical WM gets darker, near the intensity of the GM, the cortical thickness may be overestimated. Could anybody comment on this idea? I suppose there is no way of correcting this. At the same time I wonder, whether cortical atrophy in MS assessed by the FS is accurate. The cortical atrophy reported in MS by FS methods (Sailer2003) was highly focal, and I am wondering if such atrophy can reflect the wide range of disables and clinical symptoms. I would appreciate any comments to my thought. Best, Martin

2 2

Qdec correlation analyses
by Xie, Hong 12 Jan '09

12 Jan '09

Hello, freesurfer group, I have run qdec for comparing thickness between two groups. When qdec does a correlation analyses for thickness versus a second variable: 1) Does the second variable have to be a continuous interval variable or 2) can the second variable be an ordinal variable with more than 2 levels? In the case of the correlation between two continuous variable, is the test a Pearson correlation? If 2) is possible, is the correlation a Spearman correlation? Thank for your help, Hong Xie

2 7

Reusing ROIs
by Martin Kavec 12 Jan '09

12 Jan '09

Hi, For my group analysis I am thinking of reusing a specific set of cortical ROIs from already published data. I suppose that a target template (fsaverage) and ROIs itself should be sufficient to have. If I use the same fsaverage for my cohort, I should be able to get the data out of the ROIs of my subjects, and possibly compare it to the published results. Isn't it so? Thanks in advance for clarification, Martin

1 0

retinotopy and alternating stimulus direction within-run
by Jeff Phillips 12 Jan '09

12 Jan '09

Hello all, I am wondering if the FS FAST retinotopy analysis can deal with within-run alternations of stimulus direction. I have collected data in which eccentricity and polar angle were manipulated in separate runs, but within each run, a cycle of stimulation in one direction was followed by a cycle in the opposite direction. For example, 32 s of clockwise-rotating wedges were followed by 32 s of counterclockwise wedges, etc. I realize now that this may not have been a wise choice--does FS FAST have some paradigm file option for alternating stimulation? If not, is my best solution to cut and splice my runs, dividing each into two mini-runs of single-direction stimulation? Thanks, Jeff

2 1

(no subject)
by Gabriel GLZ 12 Jan '09

12 Jan '09

hello in the case that i have a ROI and i don't know wich voxeles are in there, or the coordenates of those voxeles, i want to create a specific label that only contains those voxeles, how can i do that??' _________________________________________________________________ Arrastrar y colocar: acceso muy fácil al uso compartido de fotos con Fotos de Windows Live™. http://www.microsoft.com/windows/windowslive/photos.aspx

4 4

Sulcal depth measures
by Christine Ecker 12 Jan '09

12 Jan '09

Is there any way of measuring sulcal depth with FreeSurfer? Or is sulcal depth simply measured by the positive values in ?h.sulc - i.e. negative values are 'gyral heights' and positive values are 'sulcal depths'? If so is it possible to calculate these values for certain parcellated regions such as specific sulci in aparc? Thanks for your help!

2 1

qdec X error of failed request
by Juranek, Jenifer 12 Jan '09

12 Jan '09

Hi, Running FSv405 on RHEL5. Recently obtained new error when qdec was attempted. Have successfully run qdec before on this box using FSv405. Only update made was to upgrade to FSLv412. Same error persists after restarting X. Both tkmedit and tksurfer work fine. Any ideas how to fix? Many Thanks, Jenifer [jjuranek@localhost subjects]$ qdec & [1] 4306 [jjuranek@localhost subjects]$ Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl X Error of failed request: BadMatch (invalid parameter attributes) Major opcode of failed request: 66 (X_PolySegment) Serial number of failed request: 5529 Current serial number in output stream: 5532 [1] Exit 1 qdec

2 2

accounting for BOLD response lag in FS retinotopy analysis
by Jeff Phillips 12 Jan '09

12 Jan '09

Hello all, I am performing my first retinotopy analysis, and I'd like to get some more information about the model created by paradigm files in the retinotopy analysis. Specifically, I am unsure whether to include or exclude fixation periods from the ends of my retinotopy runs. I imagine the analysis must somehow take into account the slow drop-off of the BOLD response--can you tell me if/how it does so? Since the analysis asks for the number of cycles, but not the duration of each cycle, I worry that including extra timepoints will just result in FS concluding that my stimulation period is longer than it actually is. If there exists an example design matrix for the retinotopy analysis, that would also be useful. Thanks, Jeff Phillips University of Pittsburgh

2 1

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