Hi Kay,

Kay Bente wrote:

> Hi,
>
> I still have problems converting Analyze/SPM to AFNI. I think i
> already produced several Gigabyte of rubbish, while trying to
> convert.
This is the worst part about imaging, hopefully (in about a year) a common data format will be adopted to facilitate this task....
>
> I have a high resolution anatomical dataset in saggital slices,
> data from above head up to the neck. An mean EPI image (low
> resolution, axial slices, only slices around the brain, so
> compared to the anatomical data, some slices above the brain
> are missing and the whole neck).
>
> I have a matfile from spm that registers the anatomical on the
> functional files.
>
There is a way (if I understand correctly) to have SPM write out data, transformed by the matfile. If you can do that then you should be able to go to AFNI with the anatomical and the aligned EPI to AFNI.

> OK. I created the surfaces with freesurfer and then run the
> @SUMA--- skrip to convert the freesurfer to suma and to create
> the SurfVol file.
>
> Then i used mri_convert to convert the SurfVol to analyze/spm
> mri_convert --in_type afni --out_type spm ....
> This file i used to coregister the meanEPI on the SurfVol to
> get an matfile.
You're making my stomach hurt! I suggest you don't go that route. All alignments between surfaces and volumes are done via high-resolution anatomical data sets IN AFNI"s BRICK format. Once you manage to transform your SPM functional data to align it with the anatomy you should be good to go.

cheers,
ziad