Hi Douglas,

I tried to do spatial normalization for volume data, all steps are following:

1) bbregister --mov fsubj01_rest_res_co_001.hdr --bold --s subj01 --init-fsl --reg bb_register.dat

I checked the result by tkregister2, it looked good.

2) mris_preproc --target fsaverage --hemi lh --iv fsubj01_001.hdr bb_register.dat --projfrac 0.5 --out lh.zmap.mgh

3) mri_surf2vol --surfval lh.zmap.mgh --hemi lh --identity fsaverage --outvol subj01_001.nii.gz --projfrac 0.5 --fillribbon --template wfrest_res_co_001.hdr

However, the output file subj01_001.nii.gz showed wrong orientation when viewing in MRIcron, the image looked rotated. Could you please help with it?

Best,
Xiangyu

On Mon, Apr 23, 2012 at 4:31 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
Hi Xiangyu, just add  --identity fsaverage  to the surf2vol command line
doug


On 04/19/2012 05:57 PM, Long wrote:
> Hi all,
>
> I had a question when convert a surface to volume space.
>
> First, I converted a volume nifti data to fsaverage:
>
> mris_preproc --target fsaverage --hemi lh --iv data.nii
> bb_register.dat --out data.lh.mgh
>
> Then, I want to convert the data.lh.mgh to volume space, I tried
> mri_surf2vol, however, it needs register.dat. As I understood, the
> data.lh.mgh was already registered to fsaverage surface, so how can I
> get the required register.dat file? Thank you for your attention.
>
> Best,
> Xiangyu
>
>
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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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