wow, that's good to know. Sounds like I need to add another hook so that people can set that parameter. doug
On 08/13/2012 08:24 AM, Thomas Janssens wrote: > Hi Doug, > > It seems that, our stimulus presentation is inconsistent with the way > freesurfer processes the retinotopy clockwise and counter clockwise data. > > After going through the freesurfer code I found the following. > The freesurfer code assumes that the wedge starts horizontally for > both clockwise and counterclockwise runs. > In the glm analysis, the difference between the two types of runs > (specified in the paradigm file by "neg" or "pos") is programmed in > the function $FREESURFER_HOME/fsfast/toolbox/flac_desmat.m as follows: > > for "pos" runs the real part equals cos(phz) and the imaginary > part equals sin(phz) > > for "neg" runs the real part stays cos(phz) and the imaginary > part equals -sin(phz). > > This is correct if the wedge starts in the horizontal positionm, but > not if the wedge starts vertically. > In that case the code above will lead to a phase shift of half a cycle > for the "neg" runs compared to the "pos" runs. > > However, this problem is solved by changing the code for the "neg" > runs to: the real part equals -cos(phz) and the imaginary > part equals sin(phz). > > This small change fixed the problems for our data. > > > > Thomas > > > > On 08 Aug 2012, at 16:27, Thomas Janssens wrote: > >> I am 100% sure that the stimuli themselves are correct (clockwise and >> counterclockwise/ expanding and contracting). >> >> When I look at the individual angle values I noticed that the >> difference between the cw and ccw is on average equal to half a cycle >> (so pi). >> When I plot the results (using the real.nii and imag.nii files) on a >> surface in tksurfer, I noticed that a phase offset of 0.43-0.5 seems >> to lead to a perfect match between the individually run ccw and cw. >> >> I have also tried to run the ccw runs with the pos direction in the >> par file. It is impossible to match the angle in everywhere in this >> image to the cw dataset by using an offset. >> >> Taking all this into account I would say that the pos and neg are >> correctly defined in my analysis setup. >> Could it be that freesurfer does not assume the cw and ccw to start >> both at 12 o'clock, but rather one at 12o'clock and one at 6 o'clock? >> Or do you have any idea what else is wrong? >> >> >> Thanks, >> Thomas >> >> On 06 Aug 2012, at 22:02, Douglas N Greve wrote: >> >>> I see what you mean. Is it possible that they are the same >>> direction? When you look at the angle values when running them >>> individually, are they the same or opposite sign? Are you sure that >>> the par file lists one as positive and one as negative? >>> doug >>> >>> >>> On 08/06/2012 02:56 PM, Thomas Janssens wrote: >>>> Hi Doug, >>>> >>>> the p-values are all much lower when I combine both the >>>> counterclockwise and clockwise stimuli and the angle maps look >>>> completely different. >>>> I have noticed that for the eccentricity data I have the same >>>> problem (contracting and expanding rings). >>>> >>>> Below you can find the images (it is macaque MION fMRI data). >>>> >>>> >>>> >>>> >>>> Thanks, >>>> >>>> Thomas >>>> >>>> On 06 Aug 2012, at 19:43, Douglas N Greve wrote: >>>> >>>>> what is it that is noisy? The angle map or the p-value map? Can >>>>> you send >>>>> pics? >>>>> doug >>>>> >>>>> On 08/06/2012 12:41 PM, Thomas Janssens wrote: >>>>>> Hi, >>>>>> >>>>>> I am currently analyzing some retinotopy data. >>>>>> For the polar angle stimulus we had both clockwise and >>>>>> counterclockwise stimuli. >>>>>> Both of them started at the top of the screen (12 o'clock), each >>>>>> run includes 4 full cycles and ends with the last wedge slightly >>>>>> before/after 12o'clock. >>>>>> >>>>>> We have created seperate paradigm files (direction pos / >>>>>> direction neg) for the clockwise and counterclockwise runs and >>>>>> followed the steps as indicated by the >>>>>> "FsFastIndividualRetinotopyAnalysis". >>>>>> However, when we run the Freesurfer retinotopy analysis on the >>>>>> whole data set, the polar angle is very noisy. >>>>>> When we run the same analysis separately for the clockwise and >>>>>> counterclockwise runs separately, the results look much better. >>>>>> Could anyone tell me what I am doing wrong? >>>>>> >>>>>> Thanks! >>>>>> >>>>>> Thomas >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>>>> <mailto: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 >>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>> >>>> Thomas Janssens, PhD student FWO >>>> Laboratorium voor Neuro- en Psychofysiologie >>>> K.U.Leuven Medical School >>>> Herestraat 49, B-3000 Leuven (Belgium) >>>> phone +32 16 33 00 35 >>>> cell phone +32 494 115 509 >>>> thom...@nmr.mgh.harvard.edu <mailto:thom...@nmr.mgh.harvard.edu> >>>> <mailto:thom...@nmr.mgh.harvard.edu> >>>> thomas.janss...@med.kuleuven.be >>>> <mailto:thomas.janss...@med.kuleuven.be> >>>> <mailto:thomas.janss...@med.kuleuven.be> >>>> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu <mailto: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 >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> >> >> Thomas Janssens, PhD student FWO >> Laboratorium voor Neuro- en Psychofysiologie >> K.U.Leuven Medical School >> Herestraat 49, B-3000 Leuven (Belgium) >> phone +32 16 33 00 35 >> cell phone +32 494 115 509 >> thom...@nmr.mgh.harvard.edu <mailto:thom...@nmr.mgh.harvard.edu> >> thomas.janss...@med.kuleuven.be <mailto:thomas.janss...@med.kuleuven.be> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > Thomas Janssens, PhD student FWO > Laboratorium voor Neuro- en Psychofysiologie > K.U.Leuven Medical School > Herestraat 49, B-3000 Leuven (Belgium) > phone +32 16 33 00 35 > cell phone +32 494 115 509 > thom...@nmr.mgh.harvard.edu <mailto:thom...@nmr.mgh.harvard.edu> > thomas.janss...@med.kuleuven.be <mailto:thomas.janss...@med.kuleuven.be> > -- 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.
