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!

Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program

- Bozoki Lab: Neurology/Radiology