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 -------------------------------------------------------------- sfa-sess logfile is /usr/local/freesurfer/subjects/jason/brainmapper/log/sfa-sess-bold-rtopy-1001181608.log -------------------------------------------------------------- ------------------------------------------- /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.
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>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Extension format = >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> nii >> >> >> >> hanrad = 0 >> >> >> >> >> >> >> >> >> >> >> >> ERROR: cannot determine >> >> >> >> >> >> >> >> >> >> >> >> format of 005/f
??? Attempt to reference field of non-structure array.
??? Attempt to reference field of non-structure array.
??? Attempt to reference field of non-structure array.
??? Attempt to reference field of non-structure array.
??? Undefined function or variable 'lastslice'.
??? Attempt to reference field of non-structure array.
??? Attempt to reference field of non-structure array.
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ??? Index exceeds matrix dimensions.
>> >> ??? Attempted to access tmp(NaN); index must be a positive integer or logical.
??? Attempted to access tmp(NaN); index must be a positive integer or logical.
??? Attempted to access tmp(NaN); index must be a positive integer or logical.
??? Attempted to access tmp(NaN); index must be a positive integer or logical.
??? Attempted to access tmp(NaN); index must be a positive integer or logical.
??? Attempted to access tmp(NaN); index must be a positive integer or logical.
>> >> >> >> >> >> >> >> >> >> Slice >> ??? Undefined function or variable 'lastslice'.
??? 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];
??? 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];
??? 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];
>> 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...