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