Freesurfer March 2009

freesurfer@nmr.mgh.harvard.edu

73 participants
100 discussions

active volume of surface-based analysis
by Wang, Xin 30 Mar '09

30 Mar '09

Hello, Freesurfer group, In the tutorial of surface-based fMRI analysis, the active volume are calculated from the entire depth of an given active vertex. I do not think it is the best way to measure it since no all activities occupy the entire depth of cortex. A logical way to get accurate active volume is measuring the active verities of multiple planes (e.g., at 0.1 mm distance) and then constructing the active volume from activity on these planes. A option (similar as --projfrac_max) can project the sum of all planes on the surface, and 3D active volume can be viewed in tkmedit. Does Freesurfer currently have commands to achieve something like this procedure? I am looking forward to hearing from you ASAP. Thanks, Xin

2 1

GM
by Kelly Silva 30 Mar '09

30 Mar '09

Hello, How can I calculate the GM using the FSL? Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

4 3

Incorrect correspondence in the aparc+aseg.mgz volume?
by Ryan Scotton 30 Mar '09

30 Mar '09

Hi FreeSurfers, After a months of QC'ing FreeSurfer results, my team and I are now working toward end stage analysis of our cortical thickness data. All along, we have been aiming to make improvements in the wm.mgz volume so that we can assure that the white matter and gray matter surfaces are as accurate as possible. This was under the assumption that if the white matter and gray matter surfaces are accurate, then the voxel-wise representation of the white and gray matter in the aparc+aseg.mgz file would be accurate. However, in almost all of our cases, the aparc+aseg.mgz segmentation looks very bad. The bad aparc+aseg.mgz representation of what seem to be accurate white and gray matter segmentations in the wm.mgz file is leading us to believe that the cortical correspondences created after template mapping are wrong. Does anyone else have an explanation for such a discrepancy? Is this a common problem and if so, is there any way to remedy this situation? Thanks, Ryan

3 11

sulcal width
by Prapti Gautam 30 Mar '09

30 Mar '09

Dear Freesurfers, Is there a reliable way to measure sulcal widths from T1 images using Freeesurfer? I have found information on sulcal curvatures and depth but not on width measurement and am wondering if it is possible to do so. Thanks, Prapti

2 1

GM
by Gabriel Go.Es. 30 Mar '09

30 Mar '09

hello I want to use GM volume stats, i don't know whether it is or not, where? I had understood that FS does not calculate the total GM volume, how can I make it? and can I calculate it for an individual ROI on a specific area? Regards Gabriel _________________________________________________________________ Nuevo Windows Live, un mundo lleno de posibilidades. Descúbrelo. http://www.microsoft.com/windows/windowslive/default.aspx

1 0

RE: [Freesurfer] GM
by ppj＠netfilter.com.br 30 Mar '09

30 Mar '09

Aseg.stat Sent from my Nokia phone @E71 -----Original Message----- From: Gabriel Go.Es. Sent: 30/03/2009 07:14:32 Subject: [Freesurfer] GM hello I want to use GM volume stats, i don't know whether it is or not, where? I had understood that FS does not calculate the total GM volume, how can I make it? and can I calculate it for an individual ROI on a specific area? Regards Gabriel _________________________________________________________________ Descubre todas las formas en que puedes estar en contacto con amigos y familiares. http://www.microsoft.com/windows/windowslive/default.aspx

1 0

GM
by Gabriel Go.Es. 30 Mar '09

30 Mar '09

hello I want to use GM volume stats, i don't know whether it is or not, where? I had understood that FS does not calculate the total GM volume, how can I make it? and can I calculate it for an individual ROI on a specific area? Regards Gabriel _________________________________________________________________ Descubre todas las formas en que puedes estar en contacto con amigos y familiares. http://www.microsoft.com/windows/windowslive/default.aspx

1 0

RE: Res: [Freesurfer] Doubt about GM
by ppj＠netfilter.com.br 30 Mar '09

30 Mar '09

Did you check aseg.stat Sent from my Nokia phone @E71 -----Original Message----- From: Kelly Silva Sent: 30/03/2009 05:46:36 To: Bruce Fischl Cc: freesurfer Subject: Res: [Freesurfer] Doubt about GM Hello, Thank you for your answer, Bruce. I am looking for the colheader that brings the total GM and the GM for each hemisphere, but I did not find. Can you tell me how its the file and how is the name of the variable? Thanks and regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

1 0

Doubt about GM
by Kelly Silva 30 Mar '09

30 Mar '09

Hello I´d like to know how can I calculate the GM in each hemisphere and how can I calculate the GM in specific ROIs. Thanks and best regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

2 2

Error in MRI resample?
by Pål Gunnar Larsson 27 Mar '09

27 Mar '09

I problem with a MRI set that stops recon-all very early in the process. There is a warning before : "If you find problems, please let us know", but I don't think that text is related to the error. Suggestions? Regards Pål G. Larsson

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Freesurfer March 2009