Hi Yuval,
while I have no real clue about your specific issues, it reminds e of an issue
we had in the past. We had used some condition names that start with a number
instead of a letter (e.g. 90degree) and the parsing code choked on that, as
it uses the first character of a field and tries to see whether that is a
number (as compared to taking the whole field) and that fails. (This
complication only arrises as the code tries to allow 3, 4 and 5? column formats
for the paradigm files, where the condition name lives in different columns or
so). Alas at that time we grudgingly changed our condition naming and moved on,
instead of properly fixing this and feeding the changes back to Doug (sorry for
that). So on the off-chance that this is the issue check your condition naming
inside the parameter file for numeric prefixes…
best
Sebastian
On Dec 20, 2012, at 06:00 , Yuval Harpaz wrote:
Dear FreeSurfer group
I am new to free surfer and have dificulties running fs-fast analysis for the
first time
I use freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on ubuntu but ran the
same commands for the same data on a NMR computer (nmr-stable5.0-env) which
gave the same error
the data was acquired using GE machine
I have 1 subject 2 conditions and used the below commands to process my data
running selxavg3-sess gave errors for gammafit and FIR. here is the script
and error for gammafit.
mkanalysis-sess -analysis vg.sm5.lh -surface self lh -event-related -paradigm
VG.par -polyfit 2 -nskip 0 -nconditions 2 -TR 4 -mcextreg -fsd bold -gammafit
2.25 1.25 -fwhm 5 -refeventdur 3
mkcontrast-sess -analysis vg.sm5.lh -contrast VG-vs-OE -a 2 -c 1
selxavg3-sess -s vgoe -analysis vg.sm5.lh
...
Output argument partype (and maybe others) not assigned during call to
/usr/local/freesurfer/stable5_0_0/fsfast/toolbox/fast_ldpar4.mfast_ldpar4.
Error in flac_customize (line 123)
[par partype] = fast_ldpar4(parpath);
Error in fast_selxavg3 (line 67)
flac0 = flac_customize(flac0);
for FIR the error was
ERROR: creating FIR design matrix for Condition01
??? Attempt to reference field of non-structure array.
Error in == flac_customize at 357
if(~isempty(flacnew.TFmtx))
Error in == fast_selxavg3 at 65
flac0 = flac_customize(flac0);
do you have any idea what it might be?
at some point I got complaints about NaNs in my data which are not allowed
for SVD but I cannot replicate the error
thanks
--
Yuval
Dr .Harpaz
BIU MEG lab
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