Hi,
I have an update to this query. I tried using mkanalysis-sess instead
of the ".new" version, and now I do seem to be able to get rid of
intensity normalization and prewhitening (or at least, adding these
flags now has an effect on betas/t-stats, and in the expected
directions). The code I'm using is
mkanalysis-sess -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd
bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw
40 -no-inorm -nowhiten -noautostimdur
# mkcontrast stuff here...
selxavg3-sess -sf sessid -df sessdir -analysis ToMLoc-1
However, I have a few remaining questions about the results.
1) When I look at the regressors used in the analysis, they have a
surprisingly large magnitude -- the HRF peaks at a value of ~20. Is
there any way to alter the analysis such that these peaks are
comparable to the values used in FSL/SPM, which is around .8, so that
beta values will be directly comparable across analyses? If not, I
can just scale the betas by the relevant factor, but it would be nice
if this were possible.
2) When I compare the results of this analysis to results obtained
with FSL or SPM, I find that the spatial pattern of beta/t-stats is
very similar, but the t-stats have a noticeably reduced magnitude
across the brain. Is there anything that may differ about FS-FAST's
implementation of the GLM, such that t-stats would differ?
3) I saw in a ppt presentation on FS-FAST that the option -hpf can be
used to add a highpass temporal filter to the model. However, when I
use this option with mkanalysis-new, the script says that the flag
isn't recognized. Is there another way to add such a filter?
Thanks in advance for any help. Cheers,
Ben
________________________________________
Date: Sun, 4 Sep 2011 13:15:51 -0400
From: Benjamin Matthew Deen <bd...@mit.edu>
Subject: [Freesurfer] FS-FAST modeling question
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<d0755b22ea5ed64c941ed568237aec8d1764dcc...@expo11.exchange.mit.edu>
Content-Type: text/plain; charset="us-ascii"
Hi,
I'm trying to run a model in fs-fast using no intensity normalization and no
autocorrelation correction, for the purpose of comparing results with other
software packages, and comparing results with/without autocorrelation
correction. However, I haven't been able to get this to work so far. I've
tried using the -noinorm and -nowhiten flags for mkanalysis-sess.new, but these
don't seem to have any effect on the results: noinorm doesn't change the beta
values, and nowhiten doesn't change either betas or t-stats, at all. The
commands I'm using are:
mkanalysis-sess.new -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd bold
-funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw 40 -noinorm
-nowhiten
mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope1 -a 1
-c 2
mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope2 -a 2
-c 1
mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope3 -a 1
-a 2 -c 0
mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope4 -a 0
-c 1 -c 2
selxavg3-sess -sf sessid -df sessdir -analysis ToMLoc-1
Any idea what might be going wrong, or how I can get this to work? Thanks,
Ben
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