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
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<font size="3">--------------------------<br />PhD. student Gabriel González-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email: ggonesc@upo.es<br />http://www.upo.es/neuroaging/es/</font>
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