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
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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