Chindhuri Selvadurai wrote: > 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? > No, not currently, though you can tell tkmedit/tksurfer to invert the color scale. Or you can do it by hand by multiplying the image by -1 (with fscalc). > 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 > You can just specify "-c fund" etc.
doug > 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 > > > -- 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.
