Donghoon,
I will try to reply to your question.
But I am not a SPM expert.
I would like to ask experts to correct me if I am wrong.
> 16(the bottom slice, the first acquired
> slice)-14-12-10-8-6-4-2-15-13-11-9-7-5-3-1(the last acquired slice)
Judging from your email address, I think you are working for CMU.
I have been a postdoc at CMU until last September,
so I can imagine your situation. I think you got the data
at BIRC.
(I was not able to find my new position at CMU. If I were at CMU,
I could directly talk with you.)
> The problem I concerned is whether spm take this numbers as the order.
> If I choose the user-specified mode for the sequence type in the slice
> timing option, spm ask me the sequence of slicing like this : the order of
> slices (1=bottom) ________________ .
>
> In this point, spm seems to give the number 1 to the bottom slice but the
> scanner gives it to the last slice(the top slice). So, I confused. Should
I
> give spm the reodered sequence? Or, could I use the same order as the
> header of MR image?
Please use the mumber SPM gives you, that is, the bottom=1.
If you want to the most ventral slice as the reference,
enter the number "1."
> For the reference slice, if I want to use the middle slice in order,
should
> I give 8 to spm irregardless of the actual number of image in the middle?
> or could I give 2 or 15 in the upper order?
Use the number "8" if you want to set the midle slice in TIME
to the reference slice.
But I think you might try to set the middle slice in SPACE
to the reference because it is recomended in many documents.
If so, please use the number 4, 5, 12 or 13.
If you DON'T use the first slice in TIME as the reference,
you need to change the reference time bin.
Please see Kalina's note on pre-processing for detail.
http://www-psych.stanford.edu/~kalina/SPM99/Protocols/spm99_prepros_prot.html
Gabrieli lab page is also useful.
http://gablab.stanford.edu/brainiac/
There are few people who use SPM at CMU.
Most of the people use NIS or FIASCO.
I have frequently asked this list and my friend in Japan to help.
I am afraid you are in for a wild ride. Hung in there!
Atsushi Terao
Graduate School of Education
Hokkaido University
JAPAN
P.S. Did you successfully convert original DICOM files
to the analyze format? The Siemens scanner at BIRC
use somewhat strange file name.
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