Darren,

Thanks for your thoughtful and prompt reply.

Your point about the columns of zeros and how to fix them is clear, thanks.

As far as the multiple adjustments is concerned, maybe I'm wrong, but I can't find a "fix" in the code. If you have time to bring it up with Karl, that'd be great.

Best wishes, and have a happy Thanksgiving,

Stephen J. Fromm, PhD
Contractor, NIMH/MAP
(301) 451-9265



-----Original Message-----
From: Darren Gitelman [mailto:[log in to unmask]]
Sent: Tue 11/21/2006 10:26 AM
To: Fromm, Stephen (NIH/NIMH) [C]
Cc: [log in to unmask]
Subject: RE: PPI multiple sessions
 
Hi Steve:

No clue whether they were on or off list. I had backed up the spm archives
in my email and these were the dates in the emails. I think the bottom line
was to remove a column of 0's in the null space, which solved most people's
issues, and this was implemented by Karl in SPM5. If you are using SPM2,
spm_regions v. 2.17 add the following code around line 212

xY.X0 = xY.X0(:,~~any(xY.X0));

This should come after a line with a comment "Compatibility check" and
before one that says "compute regional response..."

Jan and I had suggested different ways of accounting for the multiple
adjustments, but Karl felt they were dealt with by the fix he implemented
and I left it at that. I wonder if what should happen is that all
adjustments either take place in spm_regions (and not in spm_peb_ppi or
other functions) OR the user should have a choice of whether to adjust in
spm_peb_ppi. Perhaps I should bring this up again...?

Darren

-----Original Message-----
From: Stephen J. Fromm [mailto:[log in to unmask]]
Sent: Tuesday, November 21, 2006 8:22 AM
To: Darren G
Cc: Stephen J. Fromm
Subject: Re: PPI multiple sessions

Darren,

I've been reading some of your SPM mailbase posts re PPI with interest, but
was unable to find most of the posts (by any of the authors) you listed
below.

Is it possible that they were circulated off-list only?

I'm mainly wondering what the advice was regarding the fact that, between
spm_regions.m and spm_peb_ppi.m, effects of interest were removed twice.

Cheers,

Steve Fromm

On Fri, 28 Jul 2006 09:23:35 -0500, Darren Gitelman <d-
[log in to unmask]> wrote:

>Dear Jin
>
>This is an issue discussed on the list last year at this time (for you
SPM historians) , and I guess probably not fixed in spm2. You can search for
messages by Jan Glascher (6/20/2005, 8/24/2005, 8/25/2005), Christope
Phillips (6/23/2005, 8/22/2005), Karl Friston (6/23/2005), and I (contained
within the above posts as I do not receive back my own posts).
The bottom line is the design matrix used to adjust the data may contain
columns of 0's. Please also look at the posts from 8/22-25/2005 which
discuss the problem of "real effects of interest" vs. "effects of interest"
as defined by SPM2.
<snip>