Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

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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segmentation fault when running mris_anatomical_stats
by John Drozd 26 May '09

26 May '09

Hello, I am running the reconall steps individually for a firts try. I noticed that I get a segmentation fault when I run mris_anatomical_stats as whown below: [jdrozd@trumpet mri]$ mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -cf ../label/aparc.annot.ctab convertedfile lh INFO: assuming MGZ format for volumes. computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/wm.mgz... reading input surface /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white... reading input pial surface /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.pial... reading input white surface /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white... reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name Segmentation fault john

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Re: question about eTIV calculation
by John Drozd 26 May '09

26 May '09

Hello, I have a question about the eTIV intracranial volume calculation. My question is: Does the eTIV intracranial volume include everything interior to the outer pial surface (excluding the skull, eyes, neck and dura), and does it also include the CSF? That's all. Thank you for your time. john drozd

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tkmedit crash loading x_skull.surf files
by Jesse Friedman 26 May '09

26 May '09

tkmedit is crashing when I try to load a particular subject's inner_skull.surf or outer_skull.surf surfaces. These files were created by the MNE software, so my apologies if this question would be better suited to mne_support. If I load from the command line I get the messages below in the terminal, and tkmedit never opens. If I load the T1 without the surface from the command line and then load the surface in the gui, tkmedit quits and I get the same message in the terminal. [vantz:bem] (nmr-std-env) tkmedit RMSCH018 T1 -surface $SUBJECTS_DIR/RMSCH018/bem/outer_skull.surf Setting subject to RMSCH018 (null): vertex 0 x coordinate nan! Does anyone know what the problem is? Thanks, Jesse bugr info: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.3.1b-20090522 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.1.6.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: vantz SUBJECTS_DIR: /space/ventzl/36/users/RespMon12C/subjects PWD: /space/ventzl/36/users/RespMon12C/subjects/RMSCH018/bem ssh vantz setenv SUBJECTS_DIR /space/ventzl/36/users/RespMon12C/subjects cd /space/ventzl/36/users/RespMon12C/subjects/RMSCH018/bem -- Jesse Friedman, B.A. Massachusetts General Hospital Martinos Center, Manoach Lab Psychiatric Neuroimaging 149 13th Street #2613 Charlestown, MA 02129 Phone: (617) 726-1908 Fax: (617) 726-4078 jessef(a)nmr.mgh.harvard.edu

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Freesurfer