do you have matlab installed? What is the result of the "getmatlab" command?
Jodie Davies-Thompson wrote: > Hi Doug, > > Thanks for your reply. I tried running the contrast you suggested and > still get the same error as shown below. I'm guessing it's a problem > with my command? What have I done wrong? > > Ultimately, I would like to show the response to each wedge as > compared to the others. However, I'm hoping to find a way to show all > 4 contrasts on the inflated brain together - hence the reason I tried > going down the retinotopy route after I couldn't get this working.... > > Jodie > --------------------------------------- > [Main@Brain1] $ mkcontrast-sess -contrast upperright -analysis > er.self.lh -ncond 4 -a 1 -c 0 > INFO: Found 4 Non-Null Conditions > INFO: Found 1 Delays > Condition Weights: 1.00000000000000000000 0 0 0 > mkcontrast -anadir er.self.lh -wcond 1.00000000000000000000 0 0 0 > -sumconds -o er.self.lh/upperright.mat -wdelay 1 -no-octave > $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ > cmtxfile er.self.lh/upperright.mat > nconds 4, wcond 1.00000000000000000000 0 0 0 > 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 1.00000000000000000000 0 0 0 > -sumconds -o er.self.lh/upperright.mat -wdelay 1 -no-octave > --------------------------------------- > > On 10/13/2011 8:40 AM, Douglas N Greve wrote: >> 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > > -- > 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 -- 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.
