Re: [Freesurfer] determining sizes of clusters on surface data

Hi Don, Thanks for your reply. I'm using the same program you mentioned. Now I understand why the cluster size in mm^2 is not a constant. I'm curious about the alpha, which is corrected p- value threshold for the cluster. In fact, is there any method to get the uncorrected p-value of the cluster

RE: [Freesurfer] determining sizes of clusters on surface data

Assuming Worsley did not make any changes to his basic method since 2003 (the version I copied), then the difference here is probably, as you said, because of the resels. If you use resels, then the cluster thresholds are in resels and the surface area of two clusters with the same number of re

Re: [Freesurfer] determining sizes of clusters on surface data

Sorry, I have not used this toolbox much. Maybe Don can chime in. doug On Fri, 3 Apr 2009, Zhong Jidan wrote: Hi, I was trying to figure out if there is any way to determine the exact size at which clusters becomes significant given a specified significance on the surface data. Then i foun

[Freesurfer] determining sizes of clusters on surface data

Hi, I was trying to figure out if there is any way to determine the exact size at which clusters becomes significant given a specified significance on the surface data. Then i found there is a subject talking about this: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2007-August/005855.ht

Re: [Freesurfer] grey/white matter volumes of cortical ROIs

I'm not sure that will work as the original label was made in tkmedit. The label needs to be transferred to the surface. There's code in mri_label2label to do this (with the --paint option), but I'm not sure it's working. Try it out and let me know. doug Nick Schmansky wrote: Jose, The mris

Re: [Freesurfer] tksurfer error

FYI, Freesurfer running with a VirtualBox on Windows is available in v4.2.0 (not yet v4.3.0) here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.2.0 Get the file FSVboxVDI_PPJ.rar and read the file README- FSVboxVDI_PPJ.txt. This was created and tested by Pedro Paulo de Magalhães Oliv

Re: [Freesurfer] grey/white matter volumes of cortical ROIs

Jose, The mris_anatomical_stats command that you show is correct. For wm values, try using mri_segstats (--help), using wmparc.mgz as input, and the --slabel arg. Nick On Thu, 2009-04-02 at 16:07 +0200, Jose Luis Cantero Lorente wrote: > Hi, > > I would like to obtain gray matter volume (not

Re: [Freesurfer] tksurfer error

It seems that you are using running this Centos inside a VMWare. TkSurfer works fine in Virtualbox (2.1.4) but I'm not sure it'll do in current vmware --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --

[Freesurfer] grey/white matter volumes of cortical ROIs

Hi, I would like to obtain gray matter volume (not thickness) values for several new cortical ROIs that I have created with tkmedit, but to my knowledge this is not straight-forward with Freesurfer. We have tried this option: mris_anatomical_stats -l ?h.name.label Is that correct for my purpo

Re: Res: [Freesurfer] Talairach

once you go through analyze it's very difficult to ensure anything about orientation. You are much better off going right from dicom to mgz On Thu, 2 Apr 2009, Kelly Silva wrote: We started with DICOM.  After we have done the conversion to the analyse (hdr-img) and further to the mgz.    

Re: [Freesurfer] Talairach

Can you try converting directly Dicom to mgz? --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.netfilter.com.br 2009/4/2 Kelly Silva > We started with DICOM. After we hav

Res: [Freesurfer] Talairach

We started with DICOM.  After we have done the conversion to the analyse (hdr-img) and further to the mgz.     Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com__

Re: [Freesurfer] Talairach

what format did you start with? On Thu, 2 Apr 2009, Kelly Silva wrote: Hello,  If we have the brains well registered en relation to the Talairach (already checked with TKregister), is there any possibilty that the hemispheres of some subjects could be changed (left hemisphere as right and righ

RES: [Freesurfer] Talairach

You mean random swap? I doubt it. I would check the original data. Sent from my Nokia phone @E71 -Msg original- De: Kelly Silva Enviada: 02/04/2009 07:23:23 Assunto: [Freesurfer] Talairach Hello,  If we have the brains well registered en relation to the Talairach (already checked wit

[Freesurfer] Talairach

Hello,  If we have the brains well registered en relation to the Talairach (already checked with TKregister), is there any possibilty that the hemispheres of some subjects could be changed (left hemisphere as right and right as left) in the posterior statistical analysis?    

RE: [Freesurfer] Measuring cortical thickness with high resolution data

Hi Nick, Thank you very much. I'll have to look into that and try to process some other volumes which might work a bit better, with less manual intervention. Are there any plans to improve Freesurfer in the (near) future so that hires data can be processed within the currently available stream?