> I have a question about the AC-PC alignment.
> In the previous version like SPM99, we have to align the anatomy image as
> fitting the AC-PC line.
> I heard that I don't have to do the AC-PC alignment in SPM5.
If you can get the images roughly aligned, then it helps. The AC does not
need to be 100% exact though (within about 2cm and about 20 degrees -
dependent on your FOV, image contrast etc). This is the same as for SPM99
and SPM2.
> But, I am worrying that I have rotated image like the attached file
> comparing to the file that I aligned in the SPM99.
> Is it OK just using this rotated image or aligning this image?
You'll need to rotate it to a similar orientation to the template data in SPM.
> If I have to align this image, do you know the exact criterions that I have
> to keep when changing?
You can do this with the Display button, by specifying a rotation around the y
axis of pi radians.
>
> Also, there are som conversion options when I transform Dicom files to
> header files with MRIcro.
> When I analyze the data with AFNI, I have to check the 'FlipX(left/right)'
> option in my data.
> Then, is it same in the case of SPM?
If you can convert using SPM5 (some, but not all DICOM files can be converted
this way), then the L/R orientations should be clearly defined and understood
by any software that uses NIfTI format. This should include AFNI. Note also
that MRICron (not MRIcro) works with NIfTI, so if there is a DICOM converter
in this, then it should put the data into a suitabe format. There are also
other tools available here:
http://idoimaging.com/cgi-sys/cgiwrap/acrabb/imaging/search.pl?search=DICOM+NIfTI
Best regards,
-John
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