retinotopy (phase analysis) of block design

Hi there AFNIers-

I’m trying to run a phase (retinotopic) analysis of a simple on-off block design. no expanding rings or rotating wedges; just a simple shape repeatedly seared into early visual cortices. i’ve run both volumetric and surface analyses of the data with normal GLM block parameters and those worked fine and i can see the shape on the inflated surface. but now i want to do a phase analysis instead (replicating another published analysis).

because my data is already aligned and more with AP, i’m trying to modify the @Proc.Surf1 demo script in the AfniRetinoDemo files. i’m just giving the script .niml and .spec files and trying to dumb down the parameters i give it. clearly it’s not working, as it’s asking for a lot more specifications that are ring or wedge-related.

thoughts on how i should proceed? perhaps @RetinoProc or 3dRetinoPhase aren’t the way to go and can’t be ‘hacked’ to do what I need? Maybe 3dNLfim with the “SineWave_AP” signal model is the way forward? But can that take AP-created .niml files? Any help would be greatly appreciated; I’m new to AFNI’s retinotopic tools. THANK YOUUU


Hi again gurus

update: so I answered my own final question and yes, 3dNLfim takes *.niml.dset files and I can view results in SUMA. However, I’m not clear how to use the SineWave_AP model properly. I know the freq of the stimuli (10 sec on, 10 sec off) but is there a way to input that so it doesn’t need to estimate the frequency parameter (as apparently SineWave_APF would)? The help doc says look in “model_sinewave_ap.c” but I can’t find that file and only a which is compiled. Again, perhaps 3dNLfim is the wrong (or too old) tool here. Any clues about that or with 3dRetinoPhase (or even 3ddelay?) would be appreciated. thanks again!

update again:

3dRetinoPhase -prefix name -spectra -Tstim 20 -phase_estimate FFT -exp pb05.*.scale.niml.dset

seems to work well and replicate what we were getting with mrTools

Good to hear. Did you look at @RetinoProc, which calls 3dRetinoPhase. If you need any help with 3dNLfim, let me know.

thanks, Daniel-

yes I’d tried @RetinoProc, but not much and now I’ll try again with newfound knowledge. it seems to do a lot, however. my idea was to specify most of the preprocessing with afni_proc and then pick up with the Retino stuff where it leaves off (e.g. I’ve been inputting pb*.scale* files into 3dRetinoPhase). do you foresee any problems with this approach? i predict the answer is “depends on what you want to do” :stuck_out_tongue: