Thanks for that Mike.
Sorry yes I meant to say that the input data is segmented, normalized and smoothed!
I'm still having a problem with the subject index prompt. If I enter 30/35 (30 subjects in first group and 35 in the second), the prompt just keeps reappearing and the message on the matlab screen is "More than 2 types of indicies entered" - I've tried other variations on entering these numbers but keep getting the same message - am I just entering them wrongly (see .gif attached of screen shot).
Thanks for your time,
Cathy
-----Original Message-----
From: Marko Wilke [mailto:[log in to unmask]]
Sent: Tuesday, July 27, 2010 12:28 AM
To: Scanlon, Cathy
Cc: [log in to unmask]
Subject: Re: [SPM] snpm: 1 scan/subj
Hi Cathy,
> I have a question regarding snpm3 (running on SPM2). Im pretty sure its a straight forward question, Im having trouble figuring how to do a simple comparison of T1 structural scans between 2 groups.
So you are aiming at performing a non-parametrical vbm-type study? In
that case, I would strongly suggest you enter the segmented data (i.e.,
GM or WM partitions) instead of the T1. I am not sure this has been done
(which does not mean it is a bad idea) but consider that, with a decent
group size and the usually required high-resolution scans, the
permutation may take a really long time.
> I select design type .... "2 Groups: Two Sample T test, 1 scan/subject". I then select all my scans. The next prompt is Enter subject Index: (A/B) .... Can you tell me what this is in reference to?
Well, it is meant to indicate to SnPM which scan belongs to which group.
If you first selected all your patients (say, 50) and then all your
controls (say, 50), then you would enter 50 A's and then 50 B's. This
gives SnPM the information necessary to shuffle the datapoints around.
Hope this helps,
Marko
--
=====================================================================
Marko Wilke (Dr.med./M.D.)
[log in to unmask]
Universitts-Kinderklinik University Children's Hospital
Abt. III (Neuropdiatrie) Dept. III (Pediatric neurology)
Hoppe-Seyler-Str. 1, D - 72076 Tbingen
Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473
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