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 model_sinewave_ap.so 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!
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.
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”