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 
------------------------------------------------------------------------

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-- 
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