Freesurfer experts,
I'm attempting to utilize an archived e-mail's contents to resample data in MNI152 to 305.
The script I'm using is as follows: *mri_vol2vol * *--mov /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz * *--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz * *--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat * *--inv --o FSL_MNI305_2mm.nii.gz* * * * * This series of commands is based on the following suggestion from Doug in a previously archived e-mail exchange from someone attempting to do something similar: *>> 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.*
However, this changing the orientation of my data - essentially all images are being rotated 90degrees so the frontal lobe is pointed straight up.
Are there any suggestions to ameliorate this problem?
Thanks!