Freesurfer May 2009

freesurfer@nmr.mgh.harvard.edu

81 participants
126 discussions

RE: [Freesurfer] Troubleshooting
by Bruce Fischl 28 May '09

28 May '09

Hi Falk, you can check the transforms via: cd $SUBJECTS_DIR/$subject/mri mri_convert -rt nearest aseg.mgz -rl $FREESURFER_HOME/average/RB_all_2008-03-26.gca -at transforms/talairach.m3z aseg_in_atlas.mgz freeview -v aseg_in_atlas.mgz:colormap=lut /homes/4/fischl/dev/freesurfer/average/RB_all_2008-03-26.gca#1:colormap=lut the mri_convert applies the nonlinear warp to the aseg and reslices it into the same voxel space as the atlas (you could use the talairach.lta to check it instead if you want, or apply it to the norm without the -rt nearest switch). Then freeview loads them both and you can switch back and forth with alt-c to see if they are in register. The #1 at the end of the gca means frame index 1, which is by convention the label with the highest prior at that location in the atlas (frame index 0 is the mean intensity of the most probably class). cheers, Bruce On Thu, 28 May 2009, Falk Lüsebrink wrote: > Hi Martin, > > Thanks for the input, but I think you got me wrong. The talairach > registration and talairach check during -autorecon1 is fine. I think the > -careg stage during -autorecon2 might fail, which "generates a > multi-dimensinal talairach transform" (mri_ca_register). And I was looking > for something like the tutorials you mentioned, however not for the > talairach registration during -autorecon1, but for mri_ca_register. > > Regards, > Falk > > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Martin Kavec > Sent: Thursday, May 28, 2009 1:31 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Troubleshooting > > Hi Falk, > > On Thursday 28 May 2009 11:56:51 Falk Lüsebrink wrote: >> 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? > > For this you can follow instruction on > > http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction > > and more specifically > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > Hope some of that may lead you to successful reconstruction. > > Best, > > Martin > > _______________________________________________ > 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 > > >

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Re: [Freesurfer] Troubleshooting
by Martin Kavec 28 May '09

28 May '09

Hi Falk, On Thursday 28 May 2009 11:56:51 Falk Lüsebrink wrote: > 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? For this you can follow instruction on http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction and more specifically http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Hope some of that may lead you to successful reconstruction. Best, Martin

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export cortical/subcortical regions to nii
by Jose Luis Cantero Lorente 28 May '09

28 May '09

Dear Freesurfers, Is it possible to export to nii format specific regions previously segmented with FS? If yes, how should I proceed with this task in the case of cortical and subcortical regions? Are they exported in the MNI space, Talairach,...? Thanks in advance. Best regards, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular 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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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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Freesurfer May 2009