It looks like you have it correct. The docs are admittedly incomplete,
but they are slowly getting updated. One of the things that is changing
is that I'm transitioning away from the isxavg programs to mri_glmfit,
which is much more flexible for doing random group and inter-group
analysis. mri_glmfit can be used in conjunction with mri_volcluster or
mri_surfcluster to perform clustering/correction for mult comparisons.
Setting thresholds for clustering is not done as part of the analysis.
Rather, it is done at the end as you may want to change these parameters.
The new work-flow will be:
1. Preprocessing, registration
2. Analysis with selxavg and stxgrinder
3. Resampling to common space (vol or surf) and concatenating
4. Group analysis with mri_glmfit
5. Clustering with mri_volcluster or mri_surfcluster
The one piece that I am refining is step 3. The surface part can be done
with mris_preproc, though I've written a new script called
isxconcat-sess which will do both the volume and the surface. I believe
this works now, but I have not tested it much.
There are more docs on using mri_glmfit and the clustering on the wiki
surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferGroupAnalysis. This is
geared towards doing surface-based thickness group studies, but it
applies to volume-based as well as fmri data.
Sorry, I know the details on this are a little sketchy. I'll fill out
the wiki more when I'm done.
doug
Avram Holmes wrote:
Dear Doug,
Thanks for your reply. As new users, we're having a little trouble
verifying that our processing steps are correct. We're really after
two things. with a third question regarding support materials:
1) Some feedback regarding whether we've completed all the steps
necessary
for a glm analysis. Based on our reading and (very limited)
experience, it
seems like the combination of the mkanalysis, mkcontrast, selxavg, and
stxgrinder steps are all we need to do this properly, and that using
isxavg will allow us to run a second-level group analysis. Is this
correct? We're concerned that we may have missed something along the way.
2) Insight into how to set cluster extents and conduct statistical
tests on the data. We're used to SPM and are struggling a bit with the
inferential side of FsFast.
3) We have been passed along the Handbook for the MGH-NMR standard
processing stream (which was put out in 2000). Do you know if there is
a more current resource? The tutorial on the Wiki is a little
incomplete and I haven't been able to chase down anything on how to
run a glm in FsFast.
Any help will be greatly appreciated.
Thanks!
Avram
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On Tue, 12 Dec 2006, Doug Greve wrote:
Just looking at your scripts, they look ok. It's hard to figure out
what "trouble viewing/interpreting the results" means.
doug
Avram Holmes wrote:
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]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
