Re: [Freesurfer] How to use FIR to get HRF shape
The FIR resolution is set with the TER parameter (-TER for mkanalysis). You can try setting the TER to something shorter than the TR. This may or may not work depending upon your jittering (it would have been betterto have optseqed the stimuli with this in mind). On 12/13/2018 12:23 PM, Lauri Tuominen wrote: > External Email - Use Caution > > I want to test if there is an increase in the HRF delay in a certain > condition. > > I would like the time resolution to be higher so that the time to peak is > measured as accurately as possible. > > I thought this would be the idea of not locking the events with the TR. Am I > completely lost here? > > Cheers! > Lauri > > > Hi Lauri, what is non-ideal about it? > doug > > On 12/06/2018 05:30 PM, Lauri Tuominen wrote: >> External Email - Use Caution >> >> Hi there, >> >> I would like to know if a condition leads to a delayed HRF peaking. >> >> To device an experiment to answer this, I collected finger tapping pilot >> data with 80 trials of 3s of tapping, and jittered ITI between 5 to 25 >> seconds, TR=1.6. >> >> The trials are not TR locked because I thought I?d sample different portions >> of the HRF during each trial. >> >> I run the mkanalysis-sess with -fir 4.8 25.6 flag and all looks to be fine. >> >> My problem is that the resulting ces.nii.gz has only 16 volumes, which >> correspond to the TR, I assume (because 25.6/1.6=16). So using this, my time >> resolution for peak detection would be 1.6, which is not what I would like >> it to be. This is obviously less than ideal for answering my research >> question. >> >> How could I get the FIR fit to each timepoint so I could reconstruct the HRF >> myself? Or would there be some other workaround / analysis? Or do I need to >> collect the data in some other way, i.e somehow sliding the TR-event locking? >> >> Additional question: what is in cesmag.nii.gz, cesmagpct.nii.gz, >> iminsig.nii.gz and minsig.nii.gz? >> >> Thanks so much again for the help >> >> Lauri Tuominen >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to use FIR to get HRF shape
External Email - Use Caution I want to test if there is an increase in the HRF delay in a certain condition. I would like the time resolution to be higher so that the time to peak is measured as accurately as possible. I thought this would be the idea of not locking the events with the TR. Am I completely lost here? Cheers! Lauri Hi Lauri, what is non-ideal about it? doug On 12/06/2018 05:30 PM, Lauri Tuominen wrote: > External Email - Use Caution > > Hi there, > > I would like to know if a condition leads to a delayed HRF peaking. > > To device an experiment to answer this, I collected finger tapping pilot data > with 80 trials of 3s of tapping, and jittered ITI between 5 to 25 seconds, > TR=1.6. > > The trials are not TR locked because I thought I?d sample different portions > of the HRF during each trial. > > I run the mkanalysis-sess with -fir 4.8 25.6 flag and all looks to be fine. > > My problem is that the resulting ces.nii.gz has only 16 volumes, which > correspond to the TR, I assume (because 25.6/1.6=16). So using this, my time > resolution for peak detection would be 1.6, which is not what I would like it > to be. This is obviously less than ideal for answering my research question. > > How could I get the FIR fit to each timepoint so I could reconstruct the HRF > myself? Or would there be some other workaround / analysis? Or do I need to > collect the data in some other way, i.e somehow sliding the TR-event locking? > > Additional question: what is in cesmag.nii.gz, cesmagpct.nii.gz, > iminsig.nii.gz and minsig.nii.gz? > > Thanks so much again for the help > > Lauri Tuominen > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to use FIR to get HRF shape
Hi Lauri, what is non-ideal about it? doug On 12/06/2018 05:30 PM, Lauri Tuominen wrote: > External Email - Use Caution > > Hi there, > > I would like to know if a condition leads to a delayed HRF peaking. > > To device an experiment to answer this, I collected finger tapping pilot data > with 80 trials of 3s of tapping, and jittered ITI between 5 to 25 seconds, > TR=1.6. > > The trials are not TR locked because I thought I’d sample different portions > of the HRF during each trial. > > I run the mkanalysis-sess with -fir 4.8 25.6 flag and all looks to be fine. > > My problem is that the resulting ces.nii.gz has only 16 volumes, which > correspond to the TR, I assume (because 25.6/1.6=16). So using this, my time > resolution for peak detection would be 1.6, which is not what I would like it > to be. This is obviously less than ideal for answering my research question. > > How could I get the FIR fit to each timepoint so I could reconstruct the HRF > myself? Or would there be some other workaround / analysis? Or do I need to > collect the data in some other way, i.e somehow sliding the TR-event locking? > > Additional question: what is in cesmag.nii.gz, cesmagpct.nii.gz, > iminsig.nii.gz and minsig.nii.gz? > > Thanks so much again for the help > > Lauri Tuominen > > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] How to use FIR to get HRF shape
External Email - Use Caution Hi there, I would like to know if a condition leads to a delayed HRF peaking. To device an experiment to answer this, I collected finger tapping pilot data with 80 trials of 3s of tapping, and jittered ITI between 5 to 25 seconds, TR=1.6. The trials are not TR locked because I thought I’d sample different portions of the HRF during each trial. I run the mkanalysis-sess with -fir 4.8 25.6 flag and all looks to be fine. My problem is that the resulting ces.nii.gz has only 16 volumes, which correspond to the TR, I assume (because 25.6/1.6=16). So using this, my time resolution for peak detection would be 1.6, which is not what I would like it to be. This is obviously less than ideal for answering my research question. How could I get the FIR fit to each timepoint so I could reconstruct the HRF myself? Or would there be some other workaround / analysis? Or do I need to collect the data in some other way, i.e somehow sliding the TR-event locking? Additional question: what is in cesmag.nii.gz, cesmagpct.nii.gz, iminsig.nii.gz and minsig.nii.gz? Thanks so much again for the help Lauri Tuominen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
