Dear Doug,
Thanks for your response!
Our stimuli starts with the null condition, but abblocked assumes it's the ON condition. Is there a way to invert this?
When we look at the sig maps, how do we know what the contrast is? Which condition does it think is null/task, negative/positive? From what I understand from your first e-mail, this is the opposite of what we want.
I tried looking at the surface-based analysis using tksurfer, but since there is no constrast file for abblocked, I specified all contrasts, but how do you differentiate if you have more than one?
tksurfer-sess -s PBMST08 -hemi -lh -analysis mandy_mst_v_mct_lh -call
I think perhaps it would be better for us to switch to the block design to make things "simpler"?
Thanks!!
Chindhuri
sfa-sess is depricated now (should not even be in there). Use selxavg3-sess.
doug
Chindhuri Selvadurai wrote:
Hi Doug,
For some reason, our mkanalysis-sess command only created an analysis.info file and not a .cfg file, so we can't run the abblocked analysis using sfa-sess. Do you know what might cause this?
We are using:
freesurfer v5
our subjects directory: /cluster/manoach/milton/subjects
command that was run: mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh
output that was given:
# FSBUILD freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110202 # MKAVERSION $Id: mkanalysis-sess,v 1.49.2.8 2011/01/18 17:08:22 greve Exp $ # MKACMD /usr/local/freesurfer/stable5/fsfast/bin/mkanalysis-sess -analysis mandy_mst_v_mct_lh -TR 3 -fwhm 8 -abblocked 30 -runlistfile task -surface fsaverage lh # DATE Fri Feb 4 14:36:01 EST 2011 analysis mandy_mst_v_mct_lh mcstem fmcpr fsd bold runlistfile task TR 3 RegDOF 6 RawSpace surface fsaverage lh mask brain RawFWHM 8 RawSTC none inorm 100 acfbins 0 fixacf 1 acffwhm 20 acfsvd 0 designtype abblocked nskip 0 polyfit 2 HPFCutoffHz 0 period 30
The contrasts are going to be created automatically. These will be: fund
- stands for "fundamental" - this is the F-test of the sine and cosine
components, probably what you want
fund-sin -- t-test of the sine component (this may also be useful)
fund-cos -- t-test of the cosine component (think of this like the derivative when you assume a shape)
harm -- F test on the harmonics (probably not too useful)
It is going to assume that the first condition is ON. This does not
matter for the F-tests above, but will affect the sign of the sine component.
doug
Chindhuri Selvadurai wrote:
Hello, We are trying to set up the analysis for a periodic design alternating
between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating.
Also, how do we set up the -a and -c weighting conditions if we are
using
abblocked, since it doesn't have a paradigm file? How do we specify
the
arguments for this command? Should we instead be using the -ncond and
-wcond commands?
Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Best,
Chindhuri Selvadurai
Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Best,
Chindhuri Selvadurai
Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307