JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for SPM Archives


SPM Archives

SPM Archives


SPM@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

SPM Home

SPM Home

SPM  2002

SPM 2002

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

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

From:

Rik Henson <[log in to unmask]>

Reply-To:

Rik Henson <[log in to unmask]>

Date:

Wed, 1 May 2002 09:47:25 +0100

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (135 lines) , fig2.zip (135 lines)


Raj -

Firstly, I apologise that these issues are potentially confusing.
However, they are discussed at length on pages 14-15 of the
SPM99 manual:

  http://www.fil.ion.ucl.ac.uk/spm/course/manual/man.htm

and also on the SPM mail-archive:

  http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0009&L=spm&P=R4666

In any case, I reiterate some of them below.

Secondly, Russ has already answered your general question.
As to your specific questions:

> >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 ?

With the default value of fMRI_T0 (1), SPM effectively assumes that
the session starts with the first slice of the first acquisition (a).

This will be appropriate if you slice-time correct to the first slice
acquired in time (which is what many people do).

If you slice-time correct to a later slice in time, you will need to
adjust fMRI_T0 in proportion to fMRI_T, as Russ described.


> >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.

SPM divides each TR into a finite number of timebins (that number
being fMRI_T). This creates a "high-resolution" timespace (a vector
with fMRI_T * N elements, where N is the number of scans). So
when the user enters onsets in fractions of scans, SPM creates
a delta function (in an event-related experiment) in the bin nearest
to each onset (ie, the onsets are rounded to the nearest bin).
The convolution with the basis functions is then performed this
highresolution space, before being downsampled again to create
a value for each scan (row) in the design matrix. The specific bin
that is chosen as the sample point is that given by fMRI_T0.

Attached is a WinZipped PDF of a Figure that might help explain.


> >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

This case is a bit more trickier than usual, because your TA
is much less than your TR. SPM works in TRs, so each TR
will be divided into 4.5s/fMRI_T=4.5s/16=0.28s timebins.
You have slice-time corrected to the middle of the TA (spatial
slice 1, ie the bottom slice in Analyze format). This is not
the same as the middle of the TR. Thus you need to change
the value of fMRI_T0 (in the defaults-fmri-stats menu) to:

    round ( ( (TA/2)/TR ) * fMRI_T) = 4

I hope the logic for the above will become clear.

Note that if you slice-time corrected to the first slice in time
(spatial slice 25), then you would not need to change any
defaults. The logic for shifting to the middle slice in space
only really applies for sequential (ascending/descending)
acquisitions, where any interpolation error is pushed to
the extreme (top/bottom) slices. Your interleaving means
things are not so simple, so the first slice in time might be
easier all round.

Hope this helps
Rik


--
---------------------------------------------------------

DR RICHARD HENSON
Wellcome Department of Imaging Neuroscience
& Institute of Cognitive Neuroscience
Institute of Neurology
University College London
17 Queen Square
London, WC1N 3AR
England

EMAIL:  [log in to unmask]
URL:    http://www.fil.ion.ucl.ac.uk/~rhenson

TEL1    +44 (0)20 7679 1131
TEL2   +44 (0)20 7833 7472
FAX1    +44 (0)20 7813 1420
FAX2    +44 (0)20 7813 2835
MOB     +44 (0)794 1377 345

---------------------------------------------------------
--


Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
2006
2005
2004
2003
2002
2001
2000
1999
1998


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

For help and support help@jisc.ac.uk

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager