Hi Frank, sfa-sess does not exist in version 5 of FreeSurfer because its functions have been incorporated into selxavg3-sess. It will be a lot easier to support you if you move to version 5. Unfortunately, I have been slow in getting it documented. Having said that, I think the new version is a lot easier to use. It is very similar to regular task studies, which is pretty well documented (see http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt).
For retinotopy, there are only a few deviations: 1.a. When you create the analysis, specify something like: mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -fwhm 5 -retinotopy 30 -paradigm rtopy.par where "-retinotopy 30" means that it is a retinotopy study with a period of 30 sec 1.b Run selxavg3-sess (instead of sfa-sess) 1.c Run tksurfer-sess, like tksurfer-sess -s sess -a rtopy.self.lh This will show you the eccen and polor contrasts 2.a Create a field sign (with an occipital patch) with: fieldsign-sess -a rtopy.lh -s sess -occip 2.b View the fieldsign tksurfer-sess -s sess -a rtopy.self.lh -fieldsign The above assumes that you want to analyze the data on the subject's left hemi. Make and run anther analysis for the right hemi doug f.le...@donders.ru.nl wrote: > Hi everyone, > > The e-mail included below I sent some time ago, maybe it slipped through. In > the mean time I did find out I can plot the results with tksurfer-sess like > > tksurfer-sess -s S2_FS -h rh -analysis rtopy -c polar -map h > > But then two big questions remain: > - How to interpret these color codes? > - How to threshold them on significance? > (Third one: how to interpolate them to get away from the patchy > representation?) > > The other questions stated below are also still relevant. > > Asked this before, but can we add stuff ourselves to the wiki? Found out > quite a bit about the retinotopic inner workings which I wasn't able to find > anywhere else, might help some others. > > kind regards, > > Frank > > Old topic, but it is directly related, so I'll just continue it here. > > In the end I have the spots on the right place, but now it's not clear > to me how to interpret the map. I have created three overlays (sign, > log10 * sin, log10 * cos, like mentioned in selfreq.pdf) and loaded them > all three in tksurfer. Most important question now: how to relate these > three to get one figure instead of three separate? > > Other more minor questions: > - What do the values actually mean? Apparently I can threshold on the > basis of them, but that does't make sense to do, because the direction > info is also in there, right? I should probably threshold the F-values > first, before overlaying them on the inflated brain. > - What happened to sfa-sess in the new version of freesurfer? I can't > seem to find it. > - Why does the sfa-sess script check whether amp data is present? > Looking at the script, the line that checks whether there is amplitude > data can safely be removed. > - Just like the original Sereno paper, I have 20s pre and post stimulus > presentation time. I now only use the data where the convolved DM > predicts there will be signal, so discarding the first 20s and, due to > the HRF, keeping almost the entire second 20s. Is this the correct thing > to do, or should I rather keep everything / make sure I have an exact > number of periods for each stimulus? > > Thanks a lot in advance, > > kind regards, > > Frank > > > On Mon, 2010-01-18 at 17:32 -0500, Douglas N Greve wrote: > >> If the activation is showing up in the wrong places, then that probably >> means that the registration is off. Have you checked the registration. >> >> doug >> >> f.le...@donders.ru.nl wrote: >> >>> Probably my e-mail just slipped through, so just a short notice that I >>> still have the problem with the overlay mentioned in the last e-mail: >>> >>> "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?" >>> >>> Is it possible to edit the wikipages ourselves btw? I could add some more / >>> update the info on the retinotopic mapping to help other people when I got >>> it all figured out. >>> >>> kind regards, thanks in advance, >>> >>> Frank >>> >>> ----- Original Message ----- >>> From: "f.le...@donders.ru.nl" <f.le...@fcdonders.ru.nl> >>> To: freesurfer@nmr.mgh.harvard.edu >>> Sent: Monday, January 11, 2010 9:15:43 AM GMT +01:00 Amsterdam / Berlin / >>> Bern / Rome / Stockholm / Vienna >>> Subject: Re: [Freesurfer] Retinotopic mapping of only polar data >>> >>> 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" <gr...@nmr.mgh.harvard.edu> >>> To: "Frank Leoné" <f.le...@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.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 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>> >>> > > ----- Oorspronkelijk bericht ----- > Van: "Frank Leone" <f.le...@donders.ru.nl> > Aan: "f leone" <f.le...@donders.ru.nl> > Verzonden: Woensdag 6 oktober 2010 17:16:43 GMT +01:00 Amsterdam / Berlijn / > Bern / Rome / Stockholm / Wenen > Onderwerp: [Fwd: Re: [Freesurfer] Retinotopic mapping of only polar data] > > > > -- 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 The information in this e-mail is intended only for the person to whom it is addressed. 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