Thanks Bob again:

> You can either try to figure out why the EPI is upside down and
> shifted off to lie entirely in the Superior half of the world,
> or you can fix it after its creation via to3d. You can fix it
> with the program '3drefit', using with the option '-orient
> RAS'.

This step works pretty well already. After this 3drefit -orient RAS
the correspondence between anat and epi is already pretty good.

> The directions of the coordinates may be OK then, but it
> is likely the location in space will not overlap the anatomy
> well. Depending on how badly they don't line up, you might
> have to take further steps, such as using the @Align_Centers
> script for crude registration and/or the align_epi_anat.py
> script for fine registration of EPI to SPGR.

I then first tried align_epi_anat.py alone first (because the two looks pretty matched already)

align_epi_anat.py -anat yhh_anat2+orig. -epi yhh_r1_alt+z+orig. -epi_base 0

and the results were aligned well.

Out of curiosity, I also ran @Align_Center first, followed by align_epi_anat.py, but the results were actually worse than the align_epi_anat.py only version. Hmm....

>
> Did you create this EPI dataset using Rick Reynold's DIMON
> program? If that will work for you, it's the best approach.
> However, we don't have a lot of experience with Philips DICOM
> files, so perhaps there are some problems we aren't familiar
> with.
No. I used the to3d command instead. I did give Dimon a try, but somehow the Philips Dicom format is not recognized by the Dimon command. The error message was like:

error: invalid option <fMRI10002.dcm>


>
> Finally, I see that you are using a Mac. I thought Taiwan was
> a PC-only land. Did you smuggle this computer into the island?
Huh, no there are actually still many Mac users in Taiwan, but just in terms of user percentage, most users worldwide are still PC ruled....^^