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

>
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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/