Hi Jodie, I'm still not sure what you are trying to show. If you want to show each wedge separately, then you will need four contrasts of the form "-a 1 -c 0", "-a 2 -c 0", etc. If you want to show places where a voxel responds to *any* of the four, you can use "-a 1 -a 2 -a 3 -a 4 -nosumconds". This will create an F-test (basically an OR of all the conditions). Alternatively, you can run it with "-a 1 -a 2 -a 3 -a 4". This will just add all of them together.
doug Jodie Davies-Thompson wrote: > Dear FreeSurfers, > > I am new to Freesurfer and attempting to run a very basic analysis, > but am finally stuck after trying 3 alternative ways of displaying the > data. Any help would be greatly appreciated! > > I have 4 wedges/quadrants (no expanding rings), and want to show areas > responding to each of the 4 *on an inflated brain*. tksurfer doesn't > allow multiple zstats to be presented simultaneously so overlaying the > zstats from FSL isn't an option. My next plan was to use a basic > block-related design and run contrasts, but mkcontrast-sess produced > an error which I have copied below. (Note: I also tried -ncond 4 -a 4 > -c 1 -c 2 -c 3) > > -------------------------------------------------------- > [Main@Brain1]$ mkcontrast-sess -contrast upperright -analysis > er.self.lh -ncond 4 -wcond -1 -1 -1 3 > INFO: Found 4 Non-Null Conditions > INFO: Found 1 Delays > Runtime error (func=(main), adr=3): Divide by zero > Runtime error (func=(main), adr=4): Divide by zero > Condition Weights: -1 -1 -1 3 > mkcontrast -anadir er.self.lh -wcond -1 -1 -1 3 -sumconds -o > er.self.lh/upperright.mat -wdelay 1 -nocnorm -setwcond -no-octave > $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ > cmtxfile er.self.lh/upperright.mat > nconds 4, wcond -1 -1 -1 3 > ndelays 1, wdelay 1 > ndelays 1, wpsa > sumconds 1 > sumdelays 0 > nircorr 0 > TER 0.050000 > rdelta > rtau > ERROR running mkcontrast > mkcontrast -anadir er.self.lh -wcond -1 -1 -1 3 -sumconds -o > er.self.lh/upperright.mat -wdelay 1 -nocnorm -setwcond -no-octave > ------------------------------------------------------------------------------ > > RETINOTOPY ERROR: > After the above didn't work, I then started a retinotopic analysis > using the steps on the wiki > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis), > > but as I only have wedges and no rings, in my case I only have 1 run > and one rtopy.par file - both under bold/001. However, when I try to > view the output using the commard 'tksurfer-sess -a rtopy.self.lh -s > L_quads' I get the below error. > > ------------------------------------------------------------------------------ > [Main@Brain1]$ tksurfer-sess -a rtopy.self.lh -s L_V123quads > Surface self lh > Map Surface self lh > $Id: tksurfer-sess,v 1.16.2.1 2011/04/05 22:25:15 greve Exp $ > Linux Brain1 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST > 2011 x86_64 x86_64 x86_64 GNU/Linux > Wed Oct 12 18:02:29 PDT 2011 > /usr/local/freesurfer/bin/tksurfer > > list eccen polar > ERROR: cannot find > /usr/local/freesurfer/sessions/Subj001/L_V123quads/bold/rtopy.self.lh/eccen > ------------------------------------------------------------------------------ > > I saw the suggestions on a previous thread about fooling the analysis > by copying the polar data into the eccen directory, but I'm still > confused - should be creating identical directories (ie. 002, 003, > 004) containing the identical dataset but different rtopy.par files? > All I have under rtopy.self.lh is an 'analysis.info' file. > > Any ideas? At the moment I have no way of displaying my data, and I'm > going round in circles, so any suggestions would be great! > > Thanks in advance, > Jodie > > -- > Jodie Davies-Thompson, Postdoctoral Fellow > Department of Ophthalmology & Visual Sciences > UBC/VGH Eye Care Centre > 2550 Willow Street > Vancouver, BC > Canada > V5Z 3N9 > Tel: 604-875-411 ext 69003 > ------------------------------------------------------------------------ > > _______________________________________________ > 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 _______________________________________________ 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.
