Hi Doug,
Sorry, I should have been more specific. I meant for when one looks at the resulting transformation in a sagittal view.
More specifically... Instead of this: [image: Inline image 1]
It looks more like this (though more like a 70degree shift than 90): [image: Inline image 2] The other views are obviously affected as well. Performing a dataset "nudge" using afni generally "corrects" this problem, but I'd like to prevent it from happening in the first place.
I'm suspicious that this is occurring because I'm using '*mni305.cor.mgz*' instead of '*mni305.2mm.nii.gz*' for the 'mov' command. However, I don't have the latter file anywhere in my Freesurfer directory. The former file is the closest thing I could find.
Thoughts? Paul
On Mon, Sep 30, 2013 at 5:52 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
what do you mean the frontal lobe is pointing straight up?
On 09/30/2013 02:32 PM, Paul Beach wrote:
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
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