Every time point not specified as a condition would be counted as
baseline,
right? So does that mean then, that you have a different baseline for
your
3 and 5 condition analyses?
From: "Cameron Ellis" <cameo@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] activation patterns and par files Date: Thu, 18 Oct
2007 14:50:08 -0400 (EDT)
Hi all,
I have run two different group analyses in stable3. All of the analysis
parameters between the two are identical except that one uses a paradigm
file containing three conditions and the other uses a paradigm file
containing five conditions. The first three conditions in the analysis
using the five condition paradigm file are identical to those in the
three
condition paradigm files, meaning the timing and definitions are exactly
the same. The five condition paradigm file just contains additional
conditions that were not originally defined, as additions to the three
condition paradigm files.
The problem is that the activation patterns I receive for contrasts using
only the first three conditions of the five condition paradigm files are
different from the activation patterns of contrasts using the three
condition paradigm files. I do not know why this would be. Is there
something about not defining all events that would lead to differences of
this sort? I have visually inspected all of my paradigm files so I am
sure
the only diffences between them are the additional 2 conditions in the
five condition files. I have attached images of the differences and below
are the paths to both analyses as well as the commands run to produce the
5 condition results. The three condition commands were identical except
for calling the different analysis. Any help or insight would be much
appreciated!
Cameron
3condition:
/space/troy/3/users/retrievalnewest/Controlssh+smvsnh/bold/retrievalSPMHRF/sphsmooth-rfx/sh+smvsnh
5condition:
/space/troy/3/users/retrievalnewest/Controlssh+smvsnh/bold/retrievalSPMHRF_5cond/sphsmooth-rfx/sh+smvsnh
mkanalysis-sess.new -analysis retrievalSPMHRF_5cond -TR 2.5 -paradigm
paradigmmacro5 -designtype event_related -spmhrf 0 -nconditions 5
-timewindow 25 -prestim 5 -funcstem fmcsm -taumax
30 -polyfit 2 -inorm
selxavg-sess -sf sessidall -df sesspar -analysis retrievalSPMHRF_5cond
mkcontrast-sess -contrast -sh+smvsnh -analysis retrievalSPMHRF_5cond
-ncond 5 -a 1 -a 2 -c 3
func2sph-sess -sf sessidall -df sesspar -analysis retrievalSPMHRF_5cond
sphsmooth-sess -smoothsteps 20 -analysis retrievalSPMHRF_5cond -insphdir
sph -outsphdir sphsmooth -hemi rh -sf sessidall -df sesspar
isxavg-re-sess -analysis retrievalSPMHRF_5cond -contrast sh+smvsnh -group
Controlssh+smvsnh -space sph -spacedir sphsmooth -hemi rh -sf
sessidcontrolssh+smvsnh -df sesspar
<< 3cond.jpg >>
<< 5cond.jpg >>
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