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 >>> gr...@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 > gr...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
