[Freesurfer] retinotopy question
Hi all, I used a retinotopy paradigm with two horizontal and vertical wedges located at the meridians (flickering at 8Hz, switching every 20 seconds) do you think that this paradigm does fit into fsfastretinotopy analysis? I'm not sure if it makes a difference compared to rotating edges... Any suggestions? Thanks, Lars -- Lars Kuchinke, PhD Freie Universität Berlin Allgemeine Psychologie Habelschwerdter Allee 45 14195 Berlin [EMAIL PROTECTED] www.fu-berlin.de/allgpsy Tel: 030 838 55776 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] retinotopy question
hi lars, the FSFast retinotopy analysis stream is geared towards temporal phase encoded data analysis, which produces field sign maps that can be used to define area boundaries. if you opt to use stationary wedge stimuli to activate the horizontal and vertical meridian representations in visual cortex rather than the traditional phase encoding stimulus paradigm, since the vertical and horizontal meridian representations also lie along area boundaries, you can identify them in your data through a standard block design paradigm analysis. this is straightforward but outside the retinotopy stream. instead you can use 'mkanalysis-sess' and 'selxavg3-sess' as described on the fswiki. of course it is possible to interpret your periodic stimulus as temporally phase encoded and run the usual frequency analysis (i.e., 'sfa-sess'), but i think that the block design analysis is more appropriate for your data. hope this helps! -jon On Tue, 26 Jun 2007, Lars Kuchinke wrote: > Hi all, > > I used a retinotopy paradigm with two horizontal and vertical wedges located > at the meridians (flickering at 8Hz, switching every 20 seconds) > > do you think that this paradigm does fit into fsfastretinotopy analysis? I'm > not sure if it makes a difference compared to rotating edges... > Any suggestions? > > > Thanks, > Lars > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] retinotopy question
thanks Jon, i didn't know that a simple block design analysis is possible to compute the visual area boundaries... (which is the reason why I tried to fit it into the standard sfa-sess analysis)... could you explain me (shortly) what to do than with my data regards, Lars. -design info: 8hz flickering checkerbords, 20 scans at horizontal meridian, 20 scans vertical..x10 repetitions... Jonathan Polimeni schrieb: hi lars, the FSFast retinotopy analysis stream is geared towards temporal phase encoded data analysis, which produces field sign maps that can be used to define area boundaries. if you opt to use stationary wedge stimuli to activate the horizontal and vertical meridian representations in visual cortex rather than the traditional phase encoding stimulus paradigm, since the vertical and horizontal meridian representations also lie along area boundaries, you can identify them in your data through a standard block design paradigm analysis. this is straightforward but outside the retinotopy stream. instead you can use 'mkanalysis-sess' and 'selxavg3-sess' as described on the fswiki. of course it is possible to interpret your periodic stimulus as temporally phase encoded and run the usual frequency analysis (i.e., 'sfa-sess'), but i think that the block design analysis is more appropriate for your data. hope this helps! -jon Lars Kuchinke, PhD Freie Universität Berlin Allgemeine Psychologie Habelschwerdter Allee 45 14195 Berlin [EMAIL PROTECTED] www.fu-berlin.de/allgpsy Tel: 030 838 55776 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] retinotopy question
hi lars, i just checked with doug, and he agreed that, since your stimulus is periodic, 'sfa-sess' can do the job provided that you specify that the analysis should be carried out using a block design. so, for example, if the TR is 2 sec, and since each of your conditions lasts 20 TRs per epoch for a total of 10 repetitions (or 20 epochs) per run, you can define the block design with: mkblockpar -parname horiz_vs_vert_block.par -TR 2 -nperepoch 20 \ -nepochs 20 -epochid 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 then define the analysis with something like: mkanalysis-sess \ -analysis visual_meridian_block -paradigm horiz_vs_vert_block.par \ -designtype blocked -TR 2 -nconditions 2 \ -funcstem fmcsm5 -inorm -mcextreg \ -polyfit 2 -gammafit 2.25 1.25 -taumax 26 (please consult the documentation to determine how to choose the options on those last two lines.) the key here is that the design type should be specified as "blocked" (instead of "retinotopy", which implies phase encoding). in your case you can use 'sfa-sess', and for this example the command would be: sfa-sess -df sesspar -sf sessid -a visual_meridian_block -jon On Wed, 27 Jun 2007, Lars Kuchinke wrote: > thanks Jon, > > i didn't know that a simple block design analysis is possible to compute the > visual area boundaries... > (which is the reason why I tried to fit it into the standard sfa-sess > analysis)... > could you explain me (shortly) what to do than with my data > > regards, > Lars. > > -design info: 8hz flickering checkerbords, 20 scans at horizontal meridian, 20 > scans vertical..x10 repetitions... > > > > > Jonathan Polimeni schrieb: > > hi lars, > > > > the FSFast retinotopy analysis stream is geared towards temporal phase > > encoded data analysis, which produces field sign maps that can be used to > > define area boundaries. > > > > if you opt to use stationary wedge stimuli to activate the horizontal and > > vertical meridian representations in visual cortex rather than the > > traditional phase encoding stimulus paradigm, since the vertical and > > horizontal meridian representations also lie along area boundaries, you > > can identify them in your data through a standard block design paradigm > > analysis. this is straightforward but outside the retinotopy stream. > > instead you can use 'mkanalysis-sess' and 'selxavg3-sess' as described on > > the fswiki. > > > > of course it is possible to interpret your periodic stimulus as temporally > > phase encoded and run the usual frequency analysis (i.e., 'sfa-sess'), but > > i think that the block design analysis is more appropriate for your data. > > > > hope this helps! > > > > > > -jon > > > > > > > > > > > Lars Kuchinke, PhD > Freie Universität Berlin > Allgemeine Psychologie > Habelschwerdter Allee 45 > 14195 Berlin > > [EMAIL PROTECTED] > www.fu-berlin.de/allgpsy > Tel: 030 838 55776 > > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] retinotopy question
Actually, you can do it either as a simple blocked design where you specify the timing of each block as described below or as an AB-Blocked design. If they latter, then you would run mkanalysis-sess with -designtype abblocked and then use sfa-sess. If you use -designtype blocked, then you would use selxavg-sess. If you use -designtype blocked and specify an spmhrf with one derivative, then it will be very similar to the abblocked. doug Jonathan Polimeni wrote: hi lars, i just checked with doug, and he agreed that, since your stimulus is periodic, 'sfa-sess' can do the job provided that you specify that the analysis should be carried out using a block design. so, for example, if the TR is 2 sec, and since each of your conditions lasts 20 TRs per epoch for a total of 10 repetitions (or 20 epochs) per run, you can define the block design with: mkblockpar -parname horiz_vs_vert_block.par -TR 2 -nperepoch 20 \ -nepochs 20 -epochid 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 then define the analysis with something like: mkanalysis-sess \ -analysis visual_meridian_block -paradigm horiz_vs_vert_block.par \ -designtype blocked -TR 2 -nconditions 2 \ -funcstem fmcsm5 -inorm -mcextreg \ -polyfit 2 -gammafit 2.25 1.25 -taumax 26 (please consult the documentation to determine how to choose the options on those last two lines.) the key here is that the design type should be specified as "blocked" (instead of "retinotopy", which implies phase encoding). in your case you can use 'sfa-sess', and for this example the command would be: sfa-sess -df sesspar -sf sessid -a visual_meridian_block -jon On Wed, 27 Jun 2007, Lars Kuchinke wrote: thanks Jon, i didn't know that a simple block design analysis is possible to compute the visual area boundaries... (which is the reason why I tried to fit it into the standard sfa-sess analysis)... could you explain me (shortly) what to do than with my data regards, Lars. -design info: 8hz flickering checkerbords, 20 scans at horizontal meridian, 20 scans vertical..x10 repetitions... Jonathan Polimeni schrieb: hi lars, the FSFast retinotopy analysis stream is geared towards temporal phase encoded data analysis, which produces field sign maps that can be used to define area boundaries. if you opt to use stationary wedge stimuli to activate the horizontal and vertical meridian representations in visual cortex rather than the traditional phase encoding stimulus paradigm, since the vertical and horizontal meridian representations also lie along area boundaries, you can identify them in your data through a standard block design paradigm analysis. this is straightforward but outside the retinotopy stream. instead you can use 'mkanalysis-sess' and 'selxavg3-sess' as described on the fswiki. of course it is possible to interpret your periodic stimulus as temporally phase encoded and run the usual frequency analysis (i.e., 'sfa-sess'), but i think that the block design analysis is more appropriate for your data. hope this helps! -jon Lars Kuchinke, PhD Freie Universität Berlin Allgemeine Psychologie Habelschwerdter Allee 45 14195 Berlin [EMAIL PROTECTED] www.fu-berlin.de/allgpsy Tel: 030 838 55776 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] retinotopy question
thanks jonathan & doug, is it appropriate to use the avb contrast (all vs baseline ?) or do i have to compute a two-sided 1 -1 f-contrast? lars Jonathan Polimeni schrieb: hi lars, i just checked with doug, and he agreed that, since your stimulus is periodic, 'sfa-sess' can do the job provided that you specify that the analysis should be carried out using a block design. so, for example, if the TR is 2 sec, and since each of your conditions lasts 20 TRs per epoch for a total of 10 repetitions (or 20 epochs) per run, you can define the block design with: mkblockpar -parname horiz_vs_vert_block.par -TR 2 -nperepoch 20 \ -nepochs 20 -epochid 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 then define the analysis with something like: mkanalysis-sess \ -analysis visual_meridian_block -paradigm horiz_vs_vert_block.par \ -designtype blocked -TR 2 -nconditions 2 \ -funcstem fmcsm5 -inorm -mcextreg \ -polyfit 2 -gammafit 2.25 1.25 -taumax 26 (please consult the documentation to determine how to choose the options on those last two lines.) the key here is that the design type should be specified as "blocked" (instead of "retinotopy", which implies phase encoding). in your case you can use 'sfa-sess', and for this example the command would be: sfa-sess -df sesspar -sf sessid -a visual_meridian_block -jon On Wed, 27 Jun 2007, Lars Kuchinke wrote: thanks Jon, i didn't know that a simple block design analysis is possible to compute the visual area boundaries... (which is the reason why I tried to fit it into the standard sfa-sess analysis)... could you explain me (shortly) what to do than with my data regards, Lars. -design info: 8hz flickering checkerbords, 20 scans at horizontal meridian, 20 scans vertical..x10 repetitions... Jonathan Polimeni schrieb: hi lars, the FSFast retinotopy analysis stream is geared towards temporal phase encoded data analysis, which produces field sign maps that can be used to define area boundaries. if you opt to use stationary wedge stimuli to activate the horizontal and vertical meridian representations in visual cortex rather than the traditional phase encoding stimulus paradigm, since the vertical and horizontal meridian representations also lie along area boundaries, you can identify them in your data through a standard block design paradigm analysis. this is straightforward but outside the retinotopy stream. instead you can use 'mkanalysis-sess' and 'selxavg3-sess' as described on the fswiki. of course it is possible to interpret your periodic stimulus as temporally phase encoded and run the usual frequency analysis (i.e., 'sfa-sess'), but i think that the block design analysis is more appropriate for your data. hope this helps! -jon Lars Kuchinke, PhD Freie Universität Berlin Allgemeine Psychologie Habelschwerdter Allee 45 14195 Berlin [EMAIL PROTECTED] www.fu-berlin.de/allgpsy Tel: 030 838 55776 > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] retinotopy question
Use the avb, that's an F signed by the sine component of the FFT at the fundamental. On Wed, 4 Jul 2007, Lars Kuchinke wrote: thanks jonathan & doug, is it appropriate to use the avb contrast (all vs baseline ?) or do i have to compute a two-sided 1 -1 f-contrast? lars Jonathan Polimeni schrieb: hi lars, i just checked with doug, and he agreed that, since your stimulus is periodic, 'sfa-sess' can do the job provided that you specify that the analysis should be carried out using a block design. so, for example, if the TR is 2 sec, and since each of your conditions lasts 20 TRs per epoch for a total of 10 repetitions (or 20 epochs) per run, you can define the block design with: mkblockpar -parname horiz_vs_vert_block.par -TR 2 -nperepoch 20 \ -nepochs 20 -epochid 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 then define the analysis with something like: mkanalysis-sess \ -analysis visual_meridian_block -paradigm horiz_vs_vert_block.par \ -designtype blocked -TR 2 -nconditions 2 \ -funcstem fmcsm5 -inorm -mcextreg \ -polyfit 2 -gammafit 2.25 1.25 -taumax 26 (please consult the documentation to determine how to choose the options on those last two lines.) the key here is that the design type should be specified as "blocked" (instead of "retinotopy", which implies phase encoding). in your case you can use 'sfa-sess', and for this example the command would be: sfa-sess -df sesspar -sf sessid -a visual_meridian_block -jon On Wed, 27 Jun 2007, Lars Kuchinke wrote: thanks Jon, i didn't know that a simple block design analysis is possible to compute the visual area boundaries... (which is the reason why I tried to fit it into the standard sfa-sess analysis)... could you explain me (shortly) what to do than with my data regards, Lars. -design info: 8hz flickering checkerbords, 20 scans at horizontal meridian, 20 scans vertical..x10 repetitions... Jonathan Polimeni schrieb: hi lars, the FSFast retinotopy analysis stream is geared towards temporal phase encoded data analysis, which produces field sign maps that can be used to define area boundaries. if you opt to use stationary wedge stimuli to activate the horizontal and vertical meridian representations in visual cortex rather than the traditional phase encoding stimulus paradigm, since the vertical and horizontal meridian representations also lie along area boundaries, you can identify them in your data through a standard block design paradigm analysis. this is straightforward but outside the retinotopy stream. instead you can use 'mkanalysis-sess' and 'selxavg3-sess' as described on the fswiki. of course it is possible to interpret your periodic stimulus as temporally phase encoded and run the usual frequency analysis (i.e., 'sfa-sess'), but i think that the block design analysis is more appropriate for your data. hope this helps! -jon Lars Kuchinke, PhD Freie Universität Berlin Allgemeine Psychologie Habelschwerdter Allee 45 14195 Berlin [EMAIL PROTECTED] www.fu-berlin.de/allgpsy Tel: 030 838 55776 > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
