New subject: FSL and freesurfer: combine runs in volume or on surface?

18 Jan 2010


      Dear freesurfer experts:
I am new to fs-fast and I am currently running sfa-sess on some retinotopy data and I think the main error is "cannot determine format of 005/f"
I read in a previous post related to retinotopy that you need to add the full path to the .nii files and then it will work.
My question is: where do you add the full path?
Many thanks,
Jason.
Error message:
sfa-sess -analysis rtopy -s jason-functional
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sfa-sess logfile is /usr/local/freesurfer/subjects/jason/brainmapper/log/sfa-sess-bold-rtopy-1001181608.log
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/usr/local/freesurfer/subjects/jason/brainmapper/jason-functional
Mon Jan 18 16:08:48 GMT 2010
INFO (jason-functional): RunList = 005 007 012 013
--------------------------------------------------
/usr/local/freesurfer/subjects/jason/brainmapper/jason-functional/bold
selfreqavg -TR 1.5 -o rtopy/polar/h -i 005/f -i 007/f -i 012/f -cfg /usr/local/freesurfer/subjects/jason/brainmapper/rtopy/analysis.cfg -parname rtopy.par
--------------------------------------------------
--- Parsing Config File: /usr/local/freesurfer/subjects/jason/brainmapper/rtopy/analysis.cfg ---- -ncycles 15 -delay 0 -nskip 0 -fwhm 0
DirectionList: +1 -1 +1
Warning: Unable to open display 'iconic'.  You will not be able to display graphics on the screen.
< M A T L A B (R) >
                  Copyright 1984-2009 The MathWorks, Inc.
                Version 7.8.0.347 (R2009a) 64-bit (glnxa64)
                             February 12, 2009
To get started, type one of these: helpwin, helpdesk, or demo.
  For product information, visit www.mathworks.com.
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>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Extension format = 
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> nii
>> >> >> >> hanrad = 0
>> >> >> >> >> >> >> >> >> >> >> >> ERROR: cannot determine 
>> >> >> >> >> >> >> >> >> >> >> >> format of 005/f
??? Attempt to reference field of non-structure array.
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??? Attempt to reference field of non-structure array.
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??? Attempt to reference field of non-structure array.
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??? Attempt to reference field of non-structure array.
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??? Undefined function or variable 'lastslice'.
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??? Attempt to reference field of non-structure array.
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??? Attempt to reference field of non-structure array.
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>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ??? Index exceeds matrix dimensions.
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>> >> ??? Attempted to access tmp(NaN); index must be a positive integer or logical.
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??? Attempted to access tmp(NaN); index must be a positive integer or logical.
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??? Attempted to access tmp(NaN); index must be a positive integer or logical.
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??? Attempted to access tmp(NaN); index must be a positive integer or logical.
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??? Attempted to access tmp(NaN); index must be a positive integer or logical.
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??? Attempted to access tmp(NaN); index must be a positive integer or logical.
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>> >> >> >> >> >> >> >> >> >> Slice >> ??? Undefined function or variable 'lastslice'.
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??? Attempt to reference field of non-structure array.
Error in ==> MRIwrite at 94
  hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3)  mri.nframes];
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??? Attempt to reference field of non-structure array.
Error in ==> MRIwrite at 94
  hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3)  mri.nframes];
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??? Attempt to reference field of non-structure array.
Error in ==> MRIwrite at 94
  hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3)  mri.nframes];
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>> Saving header to rtopy/polar/h
selfreqavg COMPLETED
mri_convert rtopy/polar/h.nii -o rtopy/polar/h-offset.nii --frame 10 mri_convert rtopy/polar/h.nii -o rtopy/polar/h-offset.nii --frame 10
niiRead(): error opening file rtopy/polar/h.nii
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from rtopy/polar/h.nii...

fs-fast sfa-sess retinotopy error

sfa-sess -analysis rtopy -s jason-functional

sfa-sess logfile is /usr/local/freesurfer/subjects/jason/brainmapper/log/sfa-sess-bold-rtopy-1001181608.log