Hello Freesurfers, <br><br>I have Brodmann Area binary masks in the ICBM MNI 152 space, that I acquired using WFU_PickAtlas toolbox in SPM. These<br>masks are .nii files, and have a RAS orientation.<br><br>I am trying to resample these masks into the fsaverage MNI 305 space, specifically with the dimensions matching the &quot;mni305.cor.subfov2.mgz&quot;<br>
file found in the $FREESURFER_HOME/average file. This file is in the LIA orientation.<br><br>However, the mni152.register.dat file seems to be transforming volumes from the MNI 305 space to the MNI 152 Space in LAS orientation (MNI152_T1_2mm.nii in FSL).<br>
<br>Should I transform my Brodmann Area masks from the RAS orientation to a LAS orientation? If so, how can I achieve this? The RAS orientation is correct, so I know using mri_convert --out_dimension is out of the question.<br>
<br>I have tried to use <br><b>mri_label2vol --seg {BA_mask} --temp {$FREESURFER_HOME/average/mni305.cor.subfov2.mgz} --o {output_file} --reg mni152.register.dat --invertmtx</b><br><br>Also, I have tried to use the inverted matrix from mni152.register.dat and use it with <br>
<b>mri_vol2vol -mov {BA_mask} --reg {inverted_mni152.register.dat} --o {output_file} --tal --talres 2</b><br>However, the output files had interchanged posterior (P) and anterior (A), and superior (S) and interior (I) orientations.<br>
<br>What is the best way to achieve the resampling? Any guidance is really appreciated!<br><br>Regards,<br><br>Balaji Goparaju<br>