Hi everyone,
Doug: thanks a lot for the reply, that indeed worked, I now have a polar map overlayed on my inflated brain. But something seems to be amiss, because it plots it mainly on the temporal lobe, with nothing on the most dorsal slices, while actually I only scanned the 18 most dorsal (oriented along the occipital-parietal axis), sot here shouldn't be anything in the temporal or inferior frontal lobe. How can this be/where is it going wrong?
Moreover, I'm not sure on the format used by the polar map: the scale bar states it ranges from 1.18 to 1.18, but I don't see the sense in that. What will come out? Radians I pressume?
kind regards, thanks a lot in advance,
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: Friday, January 8, 2010 4:26:21 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: Re: [Freesurfer] Retinotopic mapping of only polar data
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.leone@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.leone@donders.ru.nl" f.leone@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" 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