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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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