Freesurfer

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30131 discussions

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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Where are all the segmentation names explained?
by Brain Apprentice 16 Sep '09

16 Sep '09

Hello, Generally speaking the segmentation names are self explanatory like Left-Hippocampus or 5th-Ventricle. There are some segmentation's that I am not sure what they mean like ctx-lh-unknown or ctx-lh-bankssts. Is there any place I can go that would explain these few segmentation names? Is there one place I can go that would explain all segmentation names? Thanks in advance to anyone who can help, even if the answer is that there is no such explanations so far in the FreeSurferWiki. B. Apprentice

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selecting the best structural scan
by sima chalavi 16 Sep '09

16 Sep '09

Hi Pedro, Thanks for your reply, Actually I am using 6 different sequences for scanning the same subject, so a small part of the difference could be because of randomness, but there should be a way to select the best scan from these 6 different scans. I need to know how to select the best. any suggestion? Regards, Sima. 2009/9/4 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> > Hi Sima, > I've run 6 versions of the same scan of the same subject I got some > differences too. Not so big as you found but still some differences > > Probably it's the -randomness flag in the recon-all > > Check: > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11235.html > <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11235.html> > cheers > ----------------------------------------------------------- > Pedro Paulo de M. Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > --- Novo Netfilter 3.2 www.Netfilter.com.br > --- Novo Netfilter Small Business > > > > 2009/9/4 sima chalavi <sima.chalavi(a)gmail.com> > >> >> Dear Freesurfer experts, >> >> We performed 6 different (pilot) structural scans from the same subject >> and analyzed the data using Freesurfer in order to find the best scan to >> be used in our real experiment. >> >> We have checked the Freesurfer output visually and there do not seem to be >> any problem as described in the trouble shooting manual. So all 6 scans >> manage to get through the Freesurfer process just fine. >> >> >> However, There are a lot of differences between the numerical results for >> the different scans. Please find Attached graphs of (some of ) the results >> of segmentation and parcellation of these 6 sequences from the statistical >> outputs. >> Now, the problem is how to select the best scan from these results. >> >> Does any body have a standard protocol for assessing images for analysis >> or a standard metric, e.g. goodness of fit, from the software that we can >> assess without having a gold standard? >> >> Or any other tip is also appreciated. >> >> Thanks in advance, >> >> Sima. >> >> -- Sima Chalavi, Ph.D. student King's College London Institute of Psychiatry (IoP) Box P040, De Crespigny Park London SE5 8AF. Tel:+44-2078485702 BCN Neuroimaging Center (NIC) University Medical Center Groningen Antonius Deusinglaan 2 P.O. Box 196 9713 AW Groningen www.neuroimaging-DID.com

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displaying retinotopy data with tksurfer and other questions
by Ritobrato Datta 16 Sep '09

16 Sep '09

Hello All, Many thanks for all the help that you provide to freesurfer users. I have a few questions - 1. Where do I find ch2better brain ? I want to pipe it through freesurfer all the way to register to the spherical atlas and plot functional data across subjects to it. 2. I have retinotopy data (expanding rings and wedges) for 6 subjects and I want to generate average functional eccentricity and polar angle data for these subjects in surface or sphere space. Can you tell me how do I average the functional data across subjects in the surface domain ? That will be gr8 help. 3. I was trying to plot the retinotopy data for 1 subject onto the inflated surface using tksurfer (following the instructions http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferWorkingWithD…) and am able to plot it but I am not able to fit a proper color scale and threshold to show color gradation reflecting the different phases. Can anyone please suggest what am I doing wrong ? I have attached a figure here. This is how it plots before any fiddling. 4. Also is there a way to calculate gray matter thickness of V1 in subjects after it has been registered to the spherical atlas. I have already generated V1 labels using Dr. Fischl and Dr. Hind's method. Thanks a lot for your help Ri

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