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Subject:

Re: Clarification sought on fMRI_T0, slice timing and stimulus onset timings

From:

Russ Poldrack <[log in to unmask]>

Reply-To:

Russ Poldrack <[log in to unmask]>

Date:

Tue, 30 Apr 2002 16:02:55 -0700

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (102 lines)

my understandingof this is as follows - hopefully the londoners will
weight in if I've gotten this wrong.

first, it's important to keep in mind that the statistical analysis
routines of SPM don't know anything about the reference slice that you
have chosen during slice timing acquisition.  fMRI_T0 is a variable that
allows you to set this relationship in a roundabout way.

the variables of interest in this case are as follows:
TR = the amount of time required to collect each image
fMRI_T = the number of quantiles in time into which the TR is broken
(i.e. the number of subsamples) for the purposes of creating the design
matrix
fMRI_T0 = the particular quantile that is assumed to represent the
zero-point in time during the TR.

It's probably easier to think of the quantity (fMRI_T0/fMRI_T)*TR than
to talk about fMRI_T0 alone.  (fMRI_T0/fMRI_T)*TR is basically the point
in time during the TR (in seconds) that is assumed to represent the
zero-point in time.

Thus, if TR=2, fMRI_T=16, and fMRI_T0=8, then when you say that a trial
started at experiment time 0 seconds, SPM will create the design matrix
as if that event happened at MR acquisition time = 1 second.

Coming back to the slice timing correction issue, you can see that if
the reference slice is temporally aligned with the setting of fMRI_T0
(i.e., the reference slice is the one that occurs at
[fMRI_T0/fMRI_T]/TR), then your analysis timing will match your
acquisition timing and all will be well in the world.

I hope that helps
cheers
rp

Rajeev Raizada wrote:

>Dear SPM list,
>
>I've read through the various postings to the list
>about fMRI_T0, slice timing etc., and I confess that
>there are still a couple of points that I'm not quite
>clear on.
>
>Here are my points of uncertainty.
>Any advice/clarifications would be greatly appreciated!
>
>1. I know that I'm meant to express stimulus onsets
>   in terms of TRs from the start of the session.
>
>   Does SPM think that the start of the session is:
>    (a) The time of the *first* slice in the first acquisition ?
>    (b) The time of the *reference* slice in the first acquisition ?
>
>    (I'm planning on setting the reference slice to be the
>     one that gets imaged half-way through the acquisition,
>     so (a) and (b) will not be the same.)
>
>2. I'm also not quite clear on how the value of fMRI_T0 alters the answer
>   to the above question. The definitions of fMRI_T0 that have been
>   posted to the list express it in terms of "which time bin to put into
>   the regressor". But it's not clear to me how precisely that translates
>   into how to specify stimulus onset timings. If anyone could give
>   a definition of fMRI_T0 (and fMRI_T) in terms of how they affect
>   how I should express stimulus onsets in terms of TRs from the start
>   of the session, rather than in terms of bins and regressors, then that
>   would help to make things a lot clearer for me.
>
>Many thanks in advance for any advice,
>
>Raj
>------------------------------------------------------------
>P.S. If anyone feels motivated to trudge through the details
>of my timing, here they are:
>
>Clustered volume acquisition
>TR = 4.5s
>25 slices
>Acquisition duration = 2100ms
>Time-per-slice = 84ms
>TA = (nslices-1) * time_per_slice = 2.016
>
>batch_slicetiming=[25 23 21 19 17 15 13 11 9 7 5 3 1 ...
>                   24 22 20 18 16 14 12 10 8 6 4 2];
>refslice = 1;
>
>The stimuli are speech sounds, 1.24 secs long, timed
>to onset w.r.t. the start of the first acq as follows:
>
>Onsets = 2.68 + TR*[ 0 1 2 3 4 5 ... etc ]
>
>This means that each stimulus starts and ends with 580ms
>of silent time at either end of it, to avoid masking by
>the scanner beeps.
>
>It seems to me that I should adjust these onset times
>in some way in order to take accout of when my refslice
>happens and what I set fMRI_T0 to be, but it is somewhat
>opaque to me how exactly I should do this.
>
>

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