Freesurfer October 2009

freesurfer@nmr.mgh.harvard.edu

99 participants
151 discussions

N3 -V1.0 option
by McLean John (NHS Greater Glasgow & Clyde) 11 Oct '09

11 Oct '09

Hi, I've been trying to run nu_correct with the -V1.0 and -distance option as follows: nu_correct -V1.0 -distance 50 'myinputfile.mnc' 'myoutputfile.mnc' It seems to run ok, and an output file is created, however, when i look at the corresponding .imp file, it says the Version is 0.9 I've just noticed that the other options in the .imp file, described as the -V1.0 default options in the nu_correct usage page (fwhm, shrink etc), are set to the correct parameters for v1.0, I guess this means that version 1.0 has been run ok then, right? A little reassurance would be great! Many thanks John ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSI recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere For more information and to find out how you can switch, visit www.connectingforhealth.nhs.uk/nhsmail ********************************************************************************************************************

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RES: reference paper of freesurfer...
by Pedro Paulo de Magalhaes Oliveira Jr 09 Oct '09

09 Oct '09

Yes. There are many papers. Try the section of the wiki: How to cite FreeSurfer. -- Enviado do meu celular Nokia E71 -----Msg original----- De: Gonzalo Rojas Enviado: 09/10/2009 19:07:05 Para: freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] reference paper of freesurfer... Hi: I need to put in a paper the main reference of freesurfer... Which?... I am searching it in the freesurfer wiki, but it appears many papers related to freesurfer... 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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reference paper of freesurfer...
by Gonzalo Rojas 09 Oct '09

09 Oct '09

Hi: I need to put in a paper the main reference of freesurfer... Which?... I am searching it in the freesurfer wiki, but it appears many papers related to freesurfer... 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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Validation
by Weisinger, Brian (NIH/OD) [E] 09 Oct '09

09 Oct '09

Hello, I am going to present some of my findings that I obtained with freesurfer at an upcoming meeting and was wondering if someone could tell me of a published paper that discusses the validity/reliability of sub cortical structure volumes (thalamus) that I could cite in my presentation. Thank you, Brian Weisinger

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skull stripped image with the original resolution
by Jose Luis Cantero Lorente 09 Oct '09

09 Oct '09

Hi there, would it be feasible to save to .nii the skull stripped image obtained with Freesurfer but keeping the original image resolution? As it is, Freesurfer allows you this operation, but the resultant .nii image comes with a poor resolution (8-bits) which is useless for my purpose. Thanks in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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Hemispheric orientation
by Dankner, Nathan (NIH/NIMH) [F] 09 Oct '09

09 Oct '09

Hello all, This is a rather basic question, but I've run into some problems answering it due to the fact that is seems so simple. Much of the data that I have been processing seems to have volumetric asymmetries the opposite of which would be expected, so I was curious as to how freesurfer determines which hemisphere is right and which is left. Does the orientation of the brain matter, or are there labels affixed to each hemisphere in header files? I am using afni .BRIK and .HEAD files. Any help would be appreciated. Thanks, Nathan

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Re: [Freesurfer] skull stripped image with the original resolution
by Jose Luis Cantero Lorente 09 Oct '09

09 Oct '09

Thanks, Nick. In which coordinates system are these skull stripped imaged? Is it possible to save to .nii these skull stripped images transformed to MNI coordinates? Thanks again. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/ ----- Mensaje original ----- De: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> Fecha: Viernes, Octubre 9, 2009 6:26 pm Asunto: Re: [Freesurfer] skull stripped image with the original resolution > add -odt int to the mri_convert flag: > > mri_convert -odt int brainmask.mgz brainmask.nii > > which saves the output file in 'integer' data format. > > On Fri, 2009-10-09 at 18:16 +0200, Jose Luis Cantero Lorente wrote: > > Hi there, > > > > would it be feasible to save to .nii the skull stripped image > obtained with Freesurfer but keeping the original image > resolution? As it is, Freesurfer allows you this operation, but > the resultant .nii image comes with a poor resolution (8-bits) > which is useless for my purpose. > > > > Thanks in advance. > > > > Best, > > Jose > > --- > > Jose Luis Cantero, Ph.D. > > Laboratory of Functional Neuroscience > > Department of Physiology, Anatomy, and Cell Biology > > University Pablo de Olavide > > Ctra. de Utrera, Km.1 > > 41013 - Sevilla > > - Spain - > > > > Phone: +34 954 977433 > > Fax: +34 954 349151 > > Email: jlcanlor(a)upo.es > > http://www.upo.es/neuroaging/es/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >

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Re: [Freesurfer] skull stripped image with the original resolution
by Jose Luis Cantero Lorente 09 Oct '09

09 Oct '09

MNI152 --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/ ----- Mensaje original ----- De: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Fecha: Viernes, Octubre 9, 2009 6:46 pm Asunto: Re: [Freesurfer] skull stripped image with the original resolution > which MNI? > > Jose Luis Cantero Lorente wrote: > > Thanks, Nick. > > > > In which coordinates system are these skull stripped imaged? Is > it possible to save to .nii these skull stripped images > transformed to MNI coordinates? > > > > Thanks again. > > > > Best, > > Jose > > > > --- > > Jose Luis Cantero, Ph.D. > > Laboratory of Functional Neuroscience > > Department of Physiology, Anatomy, and Cell Biology > > University Pablo de Olavide > > Ctra. de Utrera, Km.1 > > 41013 - Sevilla > > - Spain - > > > > Phone: +34 954 977433 > > Fax: +34 954 349151 > > Email: jlcanlor(a)upo.es > > http://www.upo.es/neuroaging/es/ > > > > ----- Mensaje original ----- > > De: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > > Fecha: Viernes, Octubre 9, 2009 6:26 pm > > Asunto: Re: [Freesurfer] skull stripped image with the original > resolution> > > > >> add -odt int to the mri_convert flag: > >> > >> mri_convert -odt int brainmask.mgz brainmask.nii > >> > >> which saves the output file in 'integer' data format. > >> > >> On Fri, 2009-10-09 at 18:16 +0200, Jose Luis Cantero Lorente wrote: > >> > >>> Hi there, > >>> > >>> would it be feasible to save to .nii the skull stripped image > >>> > >> obtained with Freesurfer but keeping the original image > >> resolution? As it is, Freesurfer allows you this operation, but > >> the resultant .nii image comes with a poor resolution (8-bits) > >> which is useless for my purpose. > >> > >>> Thanks in advance. > >>> > >>> Best, > >>> Jose > >>> --- > >>> Jose Luis Cantero, Ph.D. > >>> Laboratory of Functional Neuroscience > >>> Department of Physiology, Anatomy, and Cell Biology > >>> University Pablo de Olavide > >>> Ctra. de Utrera, Km.1 > >>> 41013 - Sevilla > >>> - Spain - > >>> > >>> Phone: +34 954 977433 > >>> Fax: +34 954 349151 > >>> Email: jlcanlor(a)upo.es > >>> http://www.upo.es/neuroaging/es/ > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >> > > > > _______________________________________________ > > 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 > > >

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spatial smoothing and retinotopic analyses
by Aspell Jane 09 Oct '09

09 Oct '09

Hi I spatially smoothed my data (Gaussian kernel of FWHM 5mm) prior to running retinotopy analyses. Is this a bad thing - would it have blurred the boundaries between visual areas significantly? What is the usual recommendation for spatial smoothing and retinotopic analyses? Many thanks, Jane Aspell

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Monte Carlo simulations: documentation
by c.k.tamnes＠psykologi.uio.no 09 Oct '09

09 Oct '09

Dear Freesurfer users We have run some analyses on cortical thickness using Monte Carlo simulations (mri_glmfit-sim --sim mc-z) in FS 4.50. Can anyone advice me on documentation where this procedure is described? A paper where it has been used would also be very helpfull. Best Regards Christian -- Christian K. Tamnes Center for the Study of Human Cognition Department of Psychology, University of Oslo PB 1094 Blindern, 0317 Oslo, Norway Cell ph: (+47) 97572410

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Freesurfer October 2009