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  2000

SPM 2000

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: comparision between spm96 and spm99

From:

Jesper Andersson <[log in to unmask]>

Reply-To:

Jesper Andersson <[log in to unmask]>

Date:

Mon, 07 Feb 2000 16:36:14 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (143 lines)

Dear Christine and everyone,

the following is a tentative explanation for "better" results in SPM96 than
SPM99, but I think it may also be of general interest. Therefore, even if
you are not interested in SPM96 vs. SPM99, please read on.

>
>Dear all,
>
>I still have some concerns about the comparability between the results of
>spm96 and spm99. 
>I have performed the analysis of different datasets (single subjects,
>simple motor and speech tasks, block design) with spm96 and spm99 with 
>identical preprocessing and as similar as possible modelling in the
>statistics section. I always got "better" results using spm96. 
>This means the locations of activations were basically the same. However,
>the significance was higher with spm96. At equal thresholds, there were
>(more and especially) larger clusters with spm96 (identical smoothing!).
>Altogether, activation appeared to be more robust with spm96.
>
>Can anyone comment on this impression? Did anybody else compare the
>results of the analysis using spm96 and spm99 respectively?
>

The following may, or may not, be relevant to your specific question.
However I think it may be of some interest/importance both to you and
others doing epoch related fMRI.

The way epochs are specified in SPM99 is slightly counterintuitive, which
may lead to mistakes, which may in turn lead to SPM99 results being "worse"
than SPM96 results, where these mistakes were not as easily made.

It has to do with how times (in scans) of epochs are defined, and require a
little background. 

Consider an fMRI experiment with a TR of 5 seconds and descending slice
acquisition. Furthermore consider an event (being either a true event or
onset of an epoch) occuring at time 6*TR after start of first scan. We now
want to create a regressor to put into our design matrix. From the
perspective of the first slice in the 7th image volume the event only just
occurred and the value of our regressor should be zero. On the other hand
from the perspective of the last slice the event occurred 5 seconds ago,
and the activity in the regressor should be close to its peak value (if it
is a true event). 

Hence, from the perspective of the ultimate slices the "expected" value of
the regressor is completely different, but there is only one value that can
actually go into the design matrix. It is easily realised that the "best"
regressor for the last slice is translated one TR backwards in time (up in
the design matrix images) compared with the "best" regressor for the first
slice. So, which one should we pick?

This didn't use to be too much of in issue (in SPM96) since for epochs of
>~5TR the differential sensitivity between top and bottom slices wasn't
that great. However, for event related designs one TR can make the
difference between reasonable sensitivity and no sensitivity at all so this
had to be carefully addressed in SPM99 (See e.g. Henson et al. NeuroImage,
1999;6:S125).

First of all it had to be possible to specify event/epoch onsets in
fractions of TRs, since the precision of specification would otherwise be
0.5*TR which is clearly insufficent for most TRs. Therefore regressors are
created by a supersampling given by the global variable fMRI_T (which can
be checked/altered  
through the default button) whith the "factory setting" 16. This means that
if you specify an event onset of 7.45TR it will effectively be located at
the nearest 16th of an TR, which in this case is 7.44TR. Conversely, if
fMRI_T was 1 (as implicitly in SPM96) it would effectively be located at 7TR.

Secondly it had to be defined what was meant with time zero. 
Should it be defined to mean the start of the first scan (i.e. the
acquisition of the first slice), which would make a lot of intuitive sense?
Should it be defined to mean the middle of the first scan (i.e. the
acquisition of the middle slice), which would also make quite a bit of sense?
Or should it be defined as the end of the first scan (i.e. the acquisition
of the last slice)?

The SPM-authors couldn't make up their mind so it was defined through the
global variable fMRI_T0. However the default value of fMRI_T0 is 1, which
means the BY DEFAULT TIME ZERO IS DEFINED AS THE START OF THE FIRST SCAN.
If fMRI_TO is set equal to fMRI_T it changes the definition to be the end
of the first scan.

This (the default) means that an event occurring 2TR after the start of the
first scan (which is an intuitively appealing time zero for the experiment)
should be specified as having occurred at time 2 (TR). The regressor will
then be ideal for the first slice, and hence implicitly assumes that you
have interpolated to the first slice in the slice timing module.

Here comes the point for the epoch related studies. Assume you have a
variable SOA paradigm with epoch lenghts 5 6 6 6 5 6 alternating between
conditions A (implicit baseline) and B (task). You will now be prompted for
a vector of epoch onsets given in scans. The intuitive (my intuition at
least) way of specifying these would be [6 18 29], i.e. the first epoch has
been preceeded by 5 scans and starts with the sixth. This is WRONG!!!

Remember how an event (true event or onset of epoch) was defined in time
(in TR) since start of first scan. Hence, the first epoch starts at 5TRs,
NOT 6. The vector of onsets should be [5 17 28]. Hence, the definition that
makes specification of event quite intuitive makes the definition of epochs
quite counterintuitive. 

Furthermore, as we clarified for the events above, this means that the
regressor is ideal for the first slice, and progressively worse for
consecutive slices. It would seem reasonable to sensitize oneself to the
middle slice, and the vector of onsets therefore becomes [4.5 16.5 27.5].
This is quite different from the "intuitive" vector [6 18 29], and can make
quite a bit of difference to the t-values.

My, cautious, recommendation is that you change fMRI_T0 to fMRI_T/2 which
means that you are automatically sensitized to the middle slice. 

Given that the default in the slice timing module is the middle slice this
means that events should (as is intuitive) be defined in TRs since start of
experiment. 

Fixed SOA epoch related studies are defined in an intuitive, and gives you
an automatic sensitization to the middle slice.

Variable SOA epoch related studies should still be defined bearing in mind
that epochs are defined in terms of time since start of first scan (rather
than scan#) and will be senitized to the middle slice.

I appologise for this rather lengthy excursion, but I think there is quite
a bit of scope for mistakes here. Especially since reading help texts seems
increasingly unfashionable in this point and click age. Those especially
interested in event related studies will find an earlier mail regarding
these issues in http://www.mailbase.ac.uk/lists/spm/1999-07/0154.html.
  
>Thank you, Christine Preibisch
>

					Good luck Jesper
Jesper Andersson
Wellcome Dept. of Cognitive Neurology
12 Queen Square
London WC1N 3BG
phone: 44 171 833 7484
fax: 44 171 813 1420


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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

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