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 ofthe 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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