Freesurfer October 2009

freesurfer@nmr.mgh.harvard.edu

99 participants
151 discussions

tkmedit "save main volume as.." option...
by Gonzalo Rojas 06 Oct '09

06 Oct '09

Hi: I do all the steps of the "Manual Editing" process that appears in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix, but the "save main volume as.." option appears in gray (off)... Why ?... I thought it might be a access permission related issue, but it was not... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

1 0

How to use mris_register
by Xiaojing Long 06 Oct '09

06 Oct '09

Hi, all, I am new to FreeSurfer world. I am trying to do the surface-based registration using FreeSurfer. I found a tool called mris_register, which is defined as a command registering a surface to an average surface template(or another single-subject's surface). But I don't understand how to use this command. Are the inputs often xx.sphere? I have two wm surfaces 'subj1.smoothwm' and 'subj2.smoothwm' and I want to align them. Can I use mris_register to do that? What information or parameterization are required by mris_register? Since when I run this command, I get errors saying that: "reading template parameterization from target.smoothwm HIPS unsupported No such file or directory" I don't understand what this error means. Could anyone help me? Thank you so much. Best, Xiaojing

3 7

contrast matrix of 2 factors (2x4 groups)
by Stefan Brauns 06 Oct '09

06 Oct '09

Hi all, I am trying to examine the interaction of 2 factors (2 x 4 groups) and have difficulties to find the right contrast matrix for mri_glmfit. We have patients and controls at four different aquisition sites and want to know if the changes (i.e. thickness) between patients and controls are equal in every site. so we have 8 groups: patientssite1 patientssite2 patientssite3 patientssite4 controlssite1 controlssite2 controlssite3 controlssite4 the contrast for differences between patients and controls (T-Test) would be: 1/4 1/4 1/4 1/4 -1/4 -1/4 -1/4 -1/4 the contrast to investigate if the observed measured value is equal in all sites (F-Test) would be: 1/2 -1/2 0 0 1/2 -1/2 0 0 0 1/2 -1/2 0 0 1/2 -1/2 0 0 0 1/2 -1/2 0 0 1/2 -1/2 How would the contrast matrix look like if I want to test if there is an overall interaction between site and diagnosis, i.e. does the effect of diagnosis vary by site (F-Test)? Many thanks, Stefan -- Stefan Brauns

2 1

Re: [Freesurfer] Freesurfer auto verse manual segmentation for hippocampus
by Bruce Fischl 06 Oct '09

06 Oct '09

Hi Aize, what is your definition of hippocampus? Does it coincide with our's? Is fimbria included? Alveus? Bruce On Tue, 6 Oct 2009, caoaize wrote: > > Hello Bruce, > > > > We did manual and freesurfer auto segmentation on hippocampus for 39 subjects. I attached the comparison plot here. As seen in this figure, the left hemisphere sysmatically larger from auto segmentation than from manual segmentation, except one brain, with manual slightly bigger than the auto. While is not the same for the right hemisphere. We just wonder what is behind it, is it because our image contrast, or something inside freesurfer? Do you have any comments? I will be appreciated for your reply. > > > > Aize > > _________________________________________________________________ > ÉÏWindows Live ÖÐ¹úÊ×Ò³£¬ÏÂÔØ×îÐÂ°æMessenger£¡ > http://www.windowslive.cn

1 0

skull strip...
by Gonzalo Rojas 06 Oct '09

06 Oct '09

Hi: The command: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -s <subj> only runs the skullstrip procedure ?... Which is the "clone" tool ?... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

2 1

QDEC
by Jose Soares 06 Oct '09

06 Oct '09

Hi all, I am working with QDEC and I would like to know if it is possible to do subcortical structures (e.g. hippocampus, amygdala, putamen) analyses in qdec?? I only have cortical structures mapped in my analyses. Thanks for the help, Miguel. ____________________________________________________________________________________ Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

2 1

mri_glm-sim
by Martin Kavec 06 Oct '09

06 Oct '09

I wonder how log does it ususally take to complete cluster-wise correction for multiple comparisons using mri_glm-sim. I have a group analysis of 19 subjects with 1 continuous and 1 discrete factor (two levels) and the mri_glm-sim is running now for about 4 days. Is there any way to track the progress and estimate when it may finish? Thanks in advance. Martin

1 0

[FreeSurfer] Is source code available?
by Youngsang Cho 06 Oct '09

06 Oct '09

Dear all, It seems that freesurfer's source code is open. But I couldn't find any link for source code or cvs id and password. Could anybody tell me whether the source code is available to external people for academic purpose? If it's available, where can I download the source code? Please tell me the information. Thanks, Youngsang Cho Dept. of CS KAIST

1 0

mri_nu_correct.mni intensity correction problem
by Jeff Sadino 06 Oct '09

06 Oct '09

Hello, I am running FS 3 and am having problems with auto-recon1, in particular the mri_nu_correct.mni step. My orig volume has intensities around 150-250, but my nu.mgz image has intensities all below 20. I am having errors further down the line, but I think they are all due to this step. Can anyone help me get my intensity values to work out right? Thank you! Jeff Sadino _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141664/direct/01/

1 0

freeview and annotation file
by tulu＠ms36.hinet.net 05 Oct '09

05 Oct '09

2 1

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Freesurfer October 2009