On Tue, Jun 14, 2011 at 11:46 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

To go from mni152 to the MNI305 2mm space, use

mri_vol2vol --mov mni305.2mm.nii.gz \
--targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \
--inv --o output.mni305.2mm.nii.gz

This will resample MNI152_T1_2mm.nii.gz (or anything in that space) to the mni305 2mm space.

For your application, add --interp nearest, or use

mri_label2vol --seg BA_mask.mni152.nii \
--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \
--invertmtx --o outfile.nii

doug

Balaji Goparaju wrote:

Hello Freesurfers,

I have Brodmann Area binary masks in the ICBM MNI 152 space, that I acquired using WFU_PickAtlas toolbox in SPM. These
masks are .nii files, and have a RAS orientation.

I am trying to resample these masks into the fsaverage MNI 305 space, specifically with the dimensions matching the "mni305.cor.subfov2.mgz"
file found in the $FREESURFER_HOME/average file. This file is in the LIA orientation.

However, the mni152.register.dat file seems to be transforming volumes from the MNI 305 space to the MNI 152 Space in LAS orientation (MNI152_T1_2mm.nii in FSL).

Should I transform my Brodmann Area masks from the RAS orientation to a LAS orientation? If so, how can I achieve this? The RAS orientation is correct, so I know using mri_convert --out_dimension is out of the question.

I have tried to use
*mri_label2vol --seg {BA_mask} --temp {$FREESURFER_HOME/average/mni305.cor.subfov2.mgz} --o {output_file} --reg mni152.register.dat --invertmtx*

Also, I have tried to use the inverted matrix from mni152.register.dat and use it with
*mri_vol2vol -mov {BA_mask} --reg {inverted_mni152.register.dat} --o {output_file} --tal --talres 2*
However, the output files had interchanged posterior (P) and anterior (A), and superior (S) and interior (I) orientations.

What is the best way to achieve the resampling? Any guidance is really appreciated!

Regards,

Balaji Goparaju

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Douglas N. Greve, Ph.D.
MGH-NMR Center
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