You can generate a register.dat with either fslregister-sess or spmregister-sess, or, if you have it in your version, use bbregister (note that there is not a -sess version for this yet).
You can then use mri_vol2surf to resample the h.nii file to the surface, then view it in tksurfer. You can also extract certain frames with mri_convert with the --frame option. doug f.le...@donders.ru.nl wrote: > Hi everyone, > > Still not working fully, partly because I'm missing some info on the file > formats. What I now did was a run of selfreqavg with four input polar > sessions, which ran succesfully. This gives me the expected h.nii. Now I > either want to > > - use this h file directly, using paint-sess (get message register.dat is > missing) and sliceview-sess (get message it can't determine format h-offset, > which makes sense, because it doesn't exist) > - or extract w files from the first three layers of the nii files and > superimpose them in tksurfer. I don't know how I should extract them though. > Can use the SPM surfrend functions, but I can't imagine that is the way, or > is it? > > Hopefully someone can help me along either of the two paths, I'm really eager > to see whether the retinotopic analysis worked. Thanks a lot in advance! > > kind regards, > > Frank > > ----- Original Message ----- > From: "f.le...@donders.ru.nl" <f.le...@fcdonders.ru.nl> > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Monday, January 4, 2010 9:35:51 AM GMT +01:00 Amsterdam / Berlin / Bern > / Rome / Stockholm / Vienna > Subject: Re: [Freesurfer] Retinotopic mapping of only polar data > > Hi everyone, > > I fixed it with the help of Jascha: when using the full path, e.g. > /home/frank/etc.../007/f.nii it does find them. So it is now running. Thanks > for the help! > > kind regards, > > Frank > > ----- 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: Tuesday, December 22, 2009 7:58:23 PM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: Re: [Freesurfer] Retinotopic mapping of only polar data > > 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
