[Freesurfer] GLM analysis question

[Avram Holmes]

FSFast support folks,

I am looking for some support running an analysis in FSFast. As far as we can
tell we have successfully run every step in a random effects analysis but we
are having trouble viewing/interpreting the results. I was hoping that I would
be able to post my processing stream and see if anyone would give us feedback
on what we have or haven’t done correctly (see below). My understanding is that
after I run mkanalysis-sess.new, selxavg-sess, mkcontrast-sess, stxgrinder-sess,
and isxavg-re-sess, I have fit a model to the data and I am testing the fit of
the model across our contrasts. However, I’m not seeing the expected effects
and I am wondering if I am missing a step or if my stream is not optimized. I
have spent a considerable amount of time searching the wiki page and I haven’t
been able to track down a detailed description of how to conduct and interpret
a complete GLM analysis in FSFast so I am a little unsure if I have everything
correct.

Any help would be greatly appreciated,
Avram

#! /bin/csh -f

Step1

set mypath = .
set sub = $1
mc-sess -fstem f -fmcstem fmc -s ${sub} -d ${mypath}
stc-sess -i fmc -o fmcstc -so siemens -s ${sub} -d ${mypath}
spatialsmooth-sess -i fmcstc -o fmcstcsm5 -fwhm 5 -d ${mypath} -s ${sub}
mkbrainmask-sess -s ${sub} -d ${mypath}


Step2

set analysis = 'moneygamma_test'
set subj = 'FPPREW01 FPPREW02 FPPREW03 FPPREW04 FPPREW05 FPPREW06 FPPREW07
FPPREW08 FPPREW09 FPPREW10 FPPREW11 FPPREW12 FPPREW13 FPPREW14 FPPREW15
FPPREW16 FPPREW17 FPPREW18'

mkanalysis-sess.new -analysis ${analysis} -gammafit 2.25 1.25 -TR 2.5 -paradigm
moneygame.par -designtype event-related -timewindow 30 -funcstem fmcstcsm5
-nconditions 5 -polyfit 1 -mcextreg -taumax 20 -mask brain

foreach s ($subj)
        selxavg-sess -s ${s} -d . -analysis ${analysis}
end

mkcontrast-sess -analysis ${analysis} -contrast omnibus -a 1 -a 2 -a 3 -a 4 -a 5
-c 0 -nosumconds
mkcontrast-sess -analysis ${analysis} -contrast pun_v_noinc -a 1 -c 2
mkcontrast-sess -analysis ${analysis} -contrast rew_v_noinc -a 3 -c 2
mkcontrast-sess -analysis ${analysis} -contrast pun_v_rew -a 1 -c 3
mkcontrast-sess -analysis ${analysis} -contrast rew_v_pun -a 3 -c 1

foreach s ($subj)
        autoreg-sess -d . -s ${s} -fsd bold
end


Step3

set mypath = .
set analysis = 'moneygamma_test'
set subj = 'FPPREW01 FPPREW02 FPPREW03 FPPREW04 FPPREW05 FPPREW06 FPPREW07
FPPREW08 FPPREW09 FPPREW10 FPPREW11 FPPREW12 FPPREW13 FPPREW14 FPPREW15
FPPREW16 FPPREW17 FPPREW18'

foreach s ($subj)
        stxgrinder-sess -contrast omnibus -analysis ${analysis} -s ${s} -d 
${mypath}
        stxgrinder-sess -contrast pun_v_noinc -analysis ${analysis} -s ${s} -d
${mypath}
        stxgrinder-sess -contrast rew_v_noinc -analysis ${analysis} -s ${s} -d
${mypath}
        stxgrinder-sess -contrast pun_v_rew -analysis ${analysis} -s ${s} -d 
${mypath}
        stxgrinder-sess -contrast rew_v_pun -analysis ${analysis} -s ${s} -d 
${mypath}
end

Step4

set analysis = 'moneygamma_test'
set subj = 'FPPREW01 FPPREW02 FPPREW03 FPPREW04 FPPREW05 FPPREW06 FPPREW07
FPPREW08 FPPREW09 FPPREW10 FPPREW11 FPPREW12 FPPREW13 FPPREW14 FPPREW15
FPPREW16 FPPREW17 FPPREW18'
set glist = 'GROUPLIST'
set group = 'Controls'
set contrasts = 'omnibus pun_v_noinc rew_v_noinc pun_v_rew rew_v_pun'

foreach s ($subj)
        foreach anal ($analysis)
                func2tal-sess -res 4 -analysis ${anal} -d . -s ${s}
                foreach hemi (lh rh)
                        func2sph-sess -analysis ${anal} -hemi ${hemi} -projfrac 
.3 -d . -s ${s}
                        sphsmooth-sess -smoothsteps 10 -analysis ${anal} 
-insphdir sph -outsphdir
sphsm10 -hemi ${hemi} -d . -s ${s}
                end
        end
end

foreach c ($contrasts)
        isxavg-re-sess -analysis ${analysis} -group ${group} -space tal -d . -sf
${glist} -contrast ${c}
        foreach hemi (lh rh)
                isxavg-re-sess -analysis ${analysis} -group ${group} -space sph 
-hemi ${hemi}
-d . -sf ${glist} -contrast ${c}
        end
end




~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Avram Holmes
Department of Psychology
Harvard University
1210 William James Hall      Phone:(617) 495-0790
33 Kirkland Street           Fax:(617) 495-3728
Cambridge, MA 02138, USA     Email: [EMAIL PROTECTED]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~







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