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
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.leone@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
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:
frank@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
frank@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 frank@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" greve@nmr.mgh.harvard.edu To: "Frank Leoné" f.leone@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.leone@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
Do you have read permissions to the file? If so, can you send the log file created by sfa-sess?
f.leone@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:
frank@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, Frankfrank@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 frank@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, 2009To 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" greve@nmr.mgh.harvard.edu To: "Frank Leoné" f.leone@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.leone@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
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" greve@nmr.mgh.harvard.edu To: "Frank Leoné" f.leone@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.leone@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:
frank@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, Frankfrank@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 frank@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, 2009To 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" greve@nmr.mgh.harvard.edu To: "Frank Leoné" f.leone@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.leone@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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
f.leone＠donders.ru.nl