Freesurfer September 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
131 discussions

Help
by zhenxt 17 Sep '09

17 Sep '09

Hi experts, I want to know whether Freesurfer is able to eliminate effects from the data obtained from different center with different NMR equipment. As we know, the data obtained from different MRI equipments may be quite different. Even the data from the same equipment but in different acquiring date may have more or less difference. Best regards xiantong zhen 2009-09-17 zhenxt

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voxels intensity
by africa millan 17 Sep '09

17 Sep '09

Sorry, I elaborate: I would like to know the intensity of the voxel where I'm putting the control point to check if the voxel belongs to the white matter or the grey one. Is there any freesurfer tool to know it? Af. _________________________________________________________________ Con Vodafone disfruta de Hotmail gratis en tu móvil. ¡Pruébalo! http://serviciosmoviles.es.msn.com/hotmail/vodafone.aspx

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voxels intensity
by africa millan 17 Sep '09

17 Sep '09

Hello everybody I would like to know if there is any way to check the grey intensity of each voxel using tkmedit tools.This option could help me to distinguish in a better way the white matter from the grey one.Thank you. _________________________________________________________________ Descárgate Internet Explorer 8 ¡Y gana gratis viajes con Spanair! http://www.vivelive.com/spanair

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Fwd: how to extract segmented hippocampus
by Paula Diniz 17 Sep '09

17 Sep '09

---------- Forwarded message ---------- From: Paula Diniz <paula.rejane(a)gmail.com> Date: 2009/9/17 Subject: Re: [Freesurfer] how to extract segmented hippocampus To: grojas(a)computer.org Hi! I'm using 3DSlicer. This software can read mgz files without problem. You can see the presentation attached to understand how to do the rendering. Sincerely, Paula 2009/9/17 Gonzalo Rojas Costa <grojasy(a)puc.cl> Dear Douglas: > > And how can I view (render) in 3D the hippocampus that I got frok aseg.mgz > with the mri_binarize command ?... > > Sincerely, > > > Gonzalo Rojas Costa > > > > mri_binarize with --match 17 or --match 53 will do it > > > > doug > > > > Guang Zeng wrote: > >> Hi, there, > >> > >> I'd like to extract the left and right hippocampus from aseg.mgz, so > >> basically what I want is a volume where left hippocampus have value > >> (or label) 17 and right hippocampus have value (or label) 53, all the > >> other place are zero. > >> > >> How can I do it? Using mri_threshold or mri_label2vol? > >> > >> Thanks a lot! > >> > >> Guang > >> > >> > >> > >> ------------------------------------------------------------------------ > >> Hotmail: Free, trusted and rich email service. Get it now. > >> <http://clk.atdmt.com/GBL/go/171222984/direct/01/> > >> ------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >-- > >Douglas N. Greve, Ph.D. > >MGH-NMR Center > >greve(a)nmr.mgh.harvard.edu > >Phone Number: 617-724-2358 > >Fax: 617-726-7422 > > > >In order to help us help you, please follow the steps in: > >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- ================================== Paula Rejane Beserra Diniz Bacharel em Informática Biomédica Mestre em Neurociências Doutoranda em Neurociências Universidade de São Paulo Hospital das Clínicas - Ribeirão Preto ================================== -- ================================== Paula Rejane Beserra Diniz Bacharel em Informática Biomédica Mestre em Neurociências Doutoranda em Neurociências Universidade de São Paulo Hospital das Clínicas - Ribeirão Preto ==================================

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MGZ to DICOM conversion...
by Gonzalo Rojas 16 Sep '09

16 Sep '09

Hi: How can I convert an MGZ (or Analyze or NIFTI) file to a DICOM one?... 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

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how to extract segmented hippocampus
by Guang Zeng 16 Sep '09

16 Sep '09

Hi, there, I'd like to extract the left and right hippocampus from aseg.mgz, so basically what I want is a volume where left hippocampus have value (or label) 17 and right hippocampus have value (or label) 53, all the other place are zero. How can I do it? Using mri_threshold or mri_label2vol? Thanks a lot! Guang _________________________________________________________________ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/171222984/direct/01/

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FW: questions about the surface processing stream
by Lars M. Rimol 16 Sep '09

16 Sep '09

Hi, I have a few questions about the surface processing stream: I compared ?h.orig.nofix, ?h.orig, ?h.sphere and ?h.sphere.reg files. The number of triangles and vertices changes between the first two but after that they're constant. But the numbers are different across subjects. For fsaverage the number of vertices is consistently 163 842 and the number of faces 327 680. Therefore, I assume that during the tesselation step in the processing stream, different subjects get different numbers of vertices due to differences in brain size. (And that the fsaverage numbers reflect average brain size.) Is that correct? And does this mean that the size of the faces/triangles is uniform across all locations and subjects, at least before the topology fix? Thank you! Lars M. Rimol

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Surface area of subcortical structures
by Elizabeth Selgrade 16 Sep '09

16 Sep '09

Hello, Is there a way to get the surface area of FreeSurfer subcortical structures? Thanks, Liz Selgrade

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longitudinal study
by Guang Zeng 16 Sep '09

16 Sep '09

Hi, there, I am going to run the FreeSurfer Longitudinal Stream (FS 4.5) on data from different timepoints. Do we need cross-sectionally process all time points with the default workflow, or just need run the first step of the default workflow. Thanks a lot! Guang _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/171222986/direct/01/

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segmentation problem
by Paltoglou, Aspasia E 16 Sep '09

16 Sep '09

Dear All, I am new to freesurfer and I was wondering if you could give me some advice. I run the freesurfer analysis on the anatomical scan of one subject and I noticed that in output files from wm.asegedit.mgz onwards, large part of the brain (frontal lobes) appears to be missing. I checked the previous output file (wm.seg.mgz) and seems to be fine, so there must be a problem when creating wm.asegedit.mgz. Many thanks, Aspa The University of Aberdeen is a charity registered in Scotland, No SC013683.

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Freesurfer September 2009