Freesurfer

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30084 discussions

recon-all : brainmasl.mgz missing
by Iwo Bohr 28 May '09

28 May '09

Dear Freesurfer experts, When I run recon-all batch command it did not produce all the files normally kept in subject/mri folder. Importantly brainmask.mgz file is missing, so I can't run reg-feat2anat command. Please advise me what I can do. Many thanks, Iwo Bohr, PhD School of Computing Science University of Newcastle, UK

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Troubleshooting
by Falk Lüsebrink 28 May '09

28 May '09

Hello, Im having trouble to generate a correct aseg.mgz for one volume of mine. The nu_noneck.mgz is also incorrect and therefore I think the -careg stage of autorecon2 might fail. Is there a way to do some kind quality check, like the tal-check during autorecon1, to see whether the talairach.m3z is incorrect? Are there some kind of instructions like fixing the bad output from the talairach registration? Or are there some parameters which can be adjusted to get better results? If none of this is possible in some way, would it be advisable to use the -noaseg flag? Im actually in no need for the subcortical segmentation, it would just be a plus, but the aseg.mgz is needed during the -segmentation stage to remove the cerebellum and brain stem. Maybe there even is another way to remove these structures automatically? Thanks in advance, Regards, Falk

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ROI
by Kelly Silva 28 May '09

28 May '09

Hello, I would like to know how can I create a ROI from one subcortical structure? Thanks in advance, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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source code for FreeSurfer and comparison with Neuroquant
by John Drozd 27 May '09

27 May '09

Hello, I am reviewing the papers outlined in the "FreeSurfer Analysis Pipeline Overview". I would find it helpful if I could download the source code for FreeSurfer. Please let me know if this is at all possible. Also I was wondering how different Cortech's commercial sister program to FreeSurfer called Neuroquant is from FreeSurfer? Other than Neuroquant being able to be used clinically, I was wondering if the functionality is different. Thank you for your time, John Drozd Postdoctoral Fellow Robarts Research Institute Medical Imaging Department The University of Western Ontario London, Ontario, Canada

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re. summary file
by Siddharth Srivastava 27 May '09

27 May '09

Hi everyone, I have a couple of questions regarding the contents of the summary file generated by mri_surfcluster, and would be happy to get some help. 1) The Max value column, does it represent the SPM{t} value, SPM{z} value or -log(p)[base 10]. 2) Can the Tal{x,y,z}, if adjusted for MNI, be reported as MNI coordinates of the cluster maxima? thanks, sid.

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Re: [Freesurfer] Re: Transform orig.mgz image to native space
by Flavio Seixas 26 May '09

26 May '09

Works. Thank you ! Flavio. --- On Tue, 5/26/09, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> wrote: From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Re: Transform orig.mgz image to native space To: "Flavio Seixas" <flseixas(a)yahoo.com.br> Cc: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu>, "Freesurfer Mailing List" <freesurfer(a)nmr.mgh.harvard.edu>, tosa(a)nmr.mgh.harvard.edu, "Doug Greve" <greve(a)nmr.mgh.harvard.edu> Date: Tuesday, May 26, 2009, 6:12 PM try: mri_convert orig.mgz -rl rawavg.mgz orig.nii On Tue, 2009-05-26 at 18:10 -0700, Flavio Seixas wrote: > The native data has (0.449219, 0.449219, 0.45) mm size and (512, 512, > 356) voxels. The orig.mgz has (256, 256, 256) voxels. I would like to > transform orig.mgz back to native data coordinates. > > Best Regards, > Flavio. > > > --- On Tue, 5/26/09, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: Transform orig.mgz image to native space > To: "Flavio Seixas" <flseixas(a)yahoo.com.br> > Cc: freesurfer(a)nmr.mgh.harvard.edu, tosa(a)nmr.mgh.harvard.edu, > greve(a)nmr.mgh.harvard.edu > Date: Tuesday, May 26, 2009, 5:56 PM > > the data should already be in the native space, not talairach. > > cheers, > Bruce > > On Tue, 26 May 2009, Flavio Seixas wrote: > > > Hi Hii, > > > > I'm beginner Freesurfer user. I segmented brain subcortical > structures using Freesurfer (recon-all). The process was > concluded ok. How could I convert aseg.mgz and orig.mgz back > to native space? I've tried "mri_convert orig.mgz orig.nii -ot > nii --apply_inverse_transform transforms/talairach.xfm", but > didn't work. Anyone could help me? I would appreciate any > suggestion. > > > > Thank you, > > Flávio. > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: Transform orig.mgz image to native space
by Flavio Seixas 26 May '09

26 May '09

The native data has (0.449219, 0.449219, 0.45) mm size and (512, 512, 356) voxels. The orig.mgz has (256, 256, 256) voxels. I would like to transform orig.mgz back to native data coordinates. Best Regards, Flavio. --- On Tue, 5/26/09, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: Transform orig.mgz image to native space To: "Flavio Seixas" <flseixas(a)yahoo.com.br> Cc: freesurfer(a)nmr.mgh.harvard.edu, tosa(a)nmr.mgh.harvard.edu, greve(a)nmr.mgh.harvard.edu Date: Tuesday, May 26, 2009, 5:56 PM the data should already be in the native space, not talairach. cheers, Bruce On Tue, 26 May 2009, Flavio Seixas wrote: > Hi Hii, > > I'm beginner Freesurfer user. I segmented brain subcortical structures using Freesurfer (recon-all). The process was concluded ok. How could I convert aseg.mgz and orig.mgz back to native space? I've tried "mri_convert orig.mgz orig.nii -ot nii --apply_inverse_transform transforms/talairach.xfm", but didn't work. Anyone could help me? I would appreciate any suggestion. > > Thank you, > Flávio. > > > > > >

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Transform orig.mgz image to native space
by Flavio Seixas 26 May '09

26 May '09

Hi Hii, I'm beginner Freesurfer user. I segmented brain subcortical structures using Freesurfer (recon-all). The process was concluded ok. How could I convert aseg.mgz and orig.mgz back to native space? I've tried "mri_convert orig.mgz orig.nii -ot nii --apply_inverse_transform transforms/talairach.xfm", but didn't work. Anyone could help me? I would appreciate any suggestion. Thank you, Flávio.

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when recon-all stoped
by Paula Diniz 26 May '09

26 May '09

Hi I was running recon-all -all when the computer was turned off. I can restart the recon-all in the point that it stopped?How? Thanks 2009/5/15 Paula Diniz <paula.rejane(a)gmail.com> > Hello! > > I have to convert the aseg.mgz file to a minc file, but I lost the > structure values reference. > Where I can find a convertion table or how I make to recover the structures > values reference? > > Thanks! > -- > ================================== > 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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RES: [Freesurfer] when recon-all stoped
by Pedro Paulo de Magalhaes Oliveira Junior 26 May '09

26 May '09

recon-all -s subjid -make all Enviado do meu celular Nokia -----Msg original----- De: Paula Diniz Enviada: 26/05/2009 17:47:04 Para: Freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] when recon-all stoped Hi I was running recon-all -all when the computer was turned off. I can restart the recon-all in the point that it stopped?How? Thanks 2009/5/15 Paula Diniz <paula.rejane(a)gmail.com> > Hello! > > I have to convert the aseg.mgz file to a minc file, but I lost the > structure values reference. > Where I can find a convertion table or how I make to recover the structures > values reference? > > Thanks! > -- > ================================== > 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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