I have tried several thing like opening on MriCroN and tkregister as:

tkregister2 --mov /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --targ /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --reg /root/trabajo/freesurfer/subjects/s_001/mri/transforms/reg.mni152.1mm.dat

----- Mensaje original -----
De: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Fecha: Jueves, 27 de Marzo de 2014, 5:54 pm
Asunto: Re: [Freesurfer] MNI CONVERSION PROBLEM
A: freesurfer@nmr.mgh.harvard.edu

>
> The first one should be correct. How are you visualizing it?
> What is the
> command line?
>
>
> On 03/27/2014 04:26 AM, Gabriel Gonzalez Escamilla wrote:
> > I have used both for the output of mni152reg:
> >
> > mri_vol2vol --mov
> > /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --
> targ
> > /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg
> >
> /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat
> > --inv --o
> >
> /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/mni152.orig.mgz>
> > and
> >
> > mri_vol2vol --targ
> > /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --
> mov
> > /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg
> >
> /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat
> > --o
> >
> /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/orig_in_mni152.mgz>
> > I also have tried these two commands with the output matrix of
> > bbregister s001_register.dat
> >
> >
> >
> > ----- Mensaje original -----
> > De: Douglas Greve <greve@nmr.mgh.harvard.edu>
> > Fecha: Jueves, 27 de Marzo de 2014, 4:11 am
> > Asunto: Re: [Freesurfer] MNI CONVERSION PROBLEM
> > A: freesurfer@nmr.mgh.harvard.edu
> >
> > >
> > > What is your vol2vol command line?
> > >
> > >
> >
> > >On 3/26/14 3:58 PM, Gabriel Gonzalez Escamilla wrote:
> >> >Dear FS experts,
> >> >
> >> >
> >> > I've been dealing with the conversion to MNI152 of some
> volumetric
> >> labels of my subjects extracted with mris_extract_label in FS
> v.5.1
> >> but, I've been unable to succeed.
> >> >
> >> >
> >> > I've tried bbregister and mni152reg commands, both of them
> give me
> >> an example to check at the registrations using tktegister2,
> when I
> >> use it everything seems to be OK, but when I do apply with
> >> mri_vol2vol any of the matrices to the volumetric masks, they
> appear
> >> to be rotated, I don't know how is it possible or how to fix it.
> >> >
> >> >
> >> > Any help will be really appreciated.
> >> >
> >> >
> >> > Many thanks in advanced,
> >> > Gabriel
> >>
> >> >
> >> >_______________________________________________ > Freesurfer
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> >
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> > >
> > >
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> > > to whom it is
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> >
> > -------------------------- PhD.
> student Gabriel
> > González-Escamilla Laboratory of Functional
> Neuroscience > />Department of Physiology, Anatomy, and Cell Biology />University
> > Pablo de Olavide Ctra. de Utrera, Km.1 41013 -
> Seville > />- Spain - Email: ggonesc@upo.es > />http://www.upo.es/neuroaging/es/
> >
> >
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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-------------------------- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggonesc@upo.es http://www.upo.es/neuroaging/es/