Do you have read permissions to the file? If so, can you send the log file created by sfa-sess?
f.le...@donders.ru.nl wrote: > Thanks a lot for the reply. I now bump into different problems though: it > doesn't understand my f.nii file, see below. I run: > > fr...@frank-desktop:~/PhD/data/Exp1_Saccades_phase$ sfa-sess -a rtopy -s > FSFAST_S1/ > > and I think the main error line is: > > ERROR: cannot determine format of 007/f > >>> ??? Attempt to reference field of non-structure array. >>> > > 007 is my first session (is a dir) and in there is one f.nii, which includes > all the scans of that run. . Previously I tried it with separate scan files, > but that didn't work either. So what does it expect? And will it work with > data preprocessed in SPM instead in FreeSurfer? The rest of the dir structure > is setup as specified in the guide > > Hopefully someone can help me, thanks a lot in advance, > > kind regards, > > Frank > > fr...@frank-desktop:~/PhD/data/Exp1_Saccades_phase$ mkanalysis-sess.new > -force -a rtopy -TR 2.12 -designtype retinotopy -paradigm rtopy.par -funcstem > f -ncycles 8 > INFO: analysis rtopy exists, but overwrite forced by user. > Completed successfully > fr...@frank-desktop:~/PhD/data/Exp1_Saccades_phase$ sfa-sess -a rtopy -s > FSFAST_S1/ > -------------------------------------------------------------- > sfa-sess logfile is > /home/frank/PhD/data/Exp1_Saccades_phase/log/sfa-sess-bold-rtopy-0912221252.log > -------------------------------------------------------------- > ------------------------------------------- > /home/frank/PhD/data/Exp1_Saccades_phase/FSFAST_S1 > Tue Dec 22 12:52:30 CET 2009 > INFO (FSFAST_S1): RunList = 007 008 009 010 011 > -------------------------------------------------- > /home/frank/PhD/data/Exp1_Saccades_phase/FSFAST_S1/bold > selfreqavg -TR 2.12 -o rtopy/polar/h -i 007/f -i 008/f -i 009/f -i 010/f -cfg > /home/frank/PhD/data/Exp1_Saccades_phase/rtopy/analysis.cfg -parname rtopy.par > -------------------------------------------------- > --- Parsing Config File: > /home/frank/PhD/data/Exp1_Saccades_phase/rtopy/analysis.cfg ---- > -ncycles 8 -delay 0 -nskip 0 -fwhm 0 > DirectionList: +1 +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. > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Extension format = nii >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> hanrad = 0 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ERROR: cannot determine format of 007/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 >>>>>>>>> >>> Could not open rtopy/polar/h.sfa for writing >>> > quiting matlab > 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 > > ----- Original Message ----- > From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > To: "Frank Leoné" <f.le...@donders.ru.nl> > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Wednesday, December 16, 2009 5:12:41 PM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: Re: [Freesurfer] Retinotopic mapping of only polar data > > If you run the retinotopy analysis, it will expect eccen. If it stops > without doing the polar analysis, you can "fool" it by copying the polar > data into the eccen directory. > > doug > > f.le...@donders.ru.nl wrote: > >> Dear all, >> >> I just started using FreeSurfer, specifically for retinotopic data, on the >> moment only polar data. So I followed the guide as mentioned on >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis >> . This does seem to work to some extend, except that it complains that I >> don't have eccentricity data. He is right about that, but is the analysis >> also doable with the eccentricity data? I really hope so, thanks a lot in >> advance, >> >> kind regards, >> >> Frank >> >> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
