Can you let me know when you have processed a set with the new tools? It's going to be a lot easier for me to instruct you on how to do those things.
doug f.le...@donders.ru.nl wrote: > Dear Doug, > > Thanks a lot for the reply, that really helps. I see that the new function is > more integrated with the rest of the standard analyses, so it now also wants > to do motion correction ed. it seems, so didn't run the full thing yet. > Still, if I make the pictures using the new functions, but an old h.nii, I > get the same kind of pictures, so can you maybe also help me with the > interpretation questions: > > - How to interpret the color codes / values on the inflatedsurface? > - How to threshold them on significance? > (Third one: how to interpolate them to get away from the patchy > representation?) > > You suggest to smooth the data btw, thought that wasn't standard procedure > when doing retinotopic mapping, at least not with a fwhm of 5. > > Thanks again, > > kind regards, > > Frank > > > ----- Oorspronkelijk bericht ----- > Van: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > Aan: "Frank Leoné" <f.le...@donders.ru.nl> > Cc: freesurfer@nmr.mgh.harvard.edu > Verzonden: Donderdag 14 oktober 2010 22:52:21 GMT +01:00 Amsterdam / Berlijn > / Bern / Rome / Stockholm / Wenen > Onderwerp: Re: [Freesurfer] Retinotopic mapping of only polar data] > > > 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
