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 _______________________________________________ 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.
