Hi
Rik and John make excellent points and are of course correct. I made the
same error (that of assuming a particular spatial acquisition order) while
warning about assuming a particular spatial acquisition order. :(
Sorry for any confusion. So my ultimate advice is 1) check the order that
slices are coming out of your scanner by running a sequence in which each
slice is written out separately and checking the time of acquisition and the
location in space of the slice, and 2) when in doubt about the first slice,
read in the image data and display it as John suggested by looking at slice
(:,:,1).
whew.
darren
-----Original Message-----
From: Rik Henson [mailto:[log in to unmask]]
Sent: Wednesday, November 29, 2006 3:51 AM
To: Darren Gitelman
Subject: Re: [SPM] Slice time correction: SPM5
Darren -
In SPM parlance, slice 1 is always the most inferior slice, i.e.,
closest to
the neck. This assumes the slices are acquired transversely. If the
slices
were not acquired transversely, I'm not sure the software will deal
with it
correctly (it may, I'm just not sure). According to your description
the
bottom slice in the volume is acquired first followed by all the odd
slices
until #25, then slice 2 followed by the even slices.
I hate to upset things further, but I think "slice 1" in SPM parlance
actually refers to the first slice stored in the image file, which is not
necessarily the most inferior slice.
(You can test by displaying an image and selecting "voxel space", and seeing
what slice appears at the bottom of the section displays - if the brain
inverts, it is actually the top slice that is stored first in the file, ie
"slice 1" would be the most superior slice in this case.)
This is described in the help for spm_slice_timing, and here:
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind03&L=SPM&P=R48
<http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind03&L=SPM&P=R487545&I=-3>
7545&I=-3
If I am wrong, please let me know (I haven't used slicetiming for several
years now; prefering multiple basis functions).
If I am correct though, it might be worth clarifying for the SPM helplist?
Rik
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