Can you send me you mkanalysis-sess command-line and the log file created by selxavg3-sess? It should be using a registration file called register.dof6.dat. You can check the registration with tkregister-sess. tksconcat.nii is a temporary file created by tkmedit-sess and tksurfer-sess; they are deleted after they run.
doug f.le...@donders.ru.nl wrote: > Hi Douglas, > > Thanks a lot, I made dummy data for the eccen and that worked. Last problem: > when I try to overlay the data on an inflated brain, the registration is off > (patches are frontal and in parts I didn't scan, while they for sure should > be posterior and within my actually scanned scans). > > I did create a register.dat using bbregister and it seems alright when I > check it with tkregister2. Is there anything different for the register.dat > in v5? I don't see it being referred now. I do see it refer to two other > files, which actually don't exist: > > tkmedit: Trying to open > /home/action/fraleo/Data/Exp1_Saccades_phase/S1_FS/bold/rtopy.S1_FS.rh/tksconcat.dat > surfer: Interpreting overlay volume > /home/action/fraleo/Data/Exp1_Saccades_phase/S1_FS/bold/rtopy.S1_FS.rh/tksconcat.nii > > > Also, when running the analysis, it automatically looks for a brain.S1_FS.rh > in the 001/masks directory. It isn't there though, only an > brain.fsaverage.rh.nii, so that's what I now used, but that might be the > reason it's going wrong. What should I use there? The coregistered structural? > > Thanks a lot in advance, hope to be able to solve this last little prob fast, > > Frank > > ----- Original Message ----- > From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > To: "Frank Leoné" <f.le...@donders.ru.nl>, "freesurfer" > <freesurfer@nmr.mgh.harvard.edu> > Sent: Wednesday, October 20, 2010 7:51:06 PM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: Re: [Freesurfer] Retinotopic mapping of only polar data] > > Oh, I see now. I did not read your subject line carefully. You have to > have both eccen and polar to run the retinotopy. One way around it is to > just copy the polar data and call it eccen. This is a bit of an > annoyance, I'll try to fix it in the next version. > > doug > > f.le...@donders.ru.nl wrote: > >> Yup, sure, thanks for the quick reply. See attached, >> >> Frank >> >> ----- Original Message ----- >> From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >> To: "Frank Leoné" <f.le...@donders.ru.nl> >> Sent: Tuesday, October 19, 2010 9:06:38 PM GMT +01:00 Amsterdam / Berlin / >> Bern / Rome / Stockholm / Vienna >> Subject: Re: [Freesurfer] Retinotopic mapping of only polar data] >> >> Can you send me the Xtmp.mat? >> >> f.le...@donders.ru.nl wrote: >> >> >>> Hi Doug, >>> >>> Sure I can. I bump into problems though, exactly the same problems as >>> mentioned before >>> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14953.html): >>> >>> Found 136019/147456 (92.2) voxels in mask >>> Creating Design Matrix >>> ... creation time = 0.010 sec >>> DoMCFit = 1 >>> ntptot = 686, nX = 42, DOF = 644 >>> Saving X matrix to >>> /home/action/fraleo/Data/Exp1_Saccades_phase/S1_FS/bold/rtopy.S1_FS.rh/Xtmp.mat >>> ??? Error using ==> svd >>> Input to SVD must not contain NaN or Inf. >>> >>> Error in ==> cond at 40 >>> s = svd(A); >>> >>> Error in ==> fast_selxavg3 at 247 >>> XCond = cond(XtX); >>> >>> Any ideas why this is/how I can solve this? Same result for multiple >>> subjects, not sure where it comes from. >>> >>> Thanks a lot in advance, >>> >>> 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: Monday, October 18, 2010 5:08:42 PM GMT +01:00 Amsterdam / Berlin / >>> Bern / Rome / Stockholm / Vienna >>> Subject: Re: [Freesurfer] Retinotopic mapping of only polar data] >>> >>> 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.
