Hi,

This may be a question for Liv Faull who has been extremely helpful to me getting my pre-processing model set up, however I thought I would post it here in case it's a more general question!

This is resting state data.

Steps of model so far:

Ran PNM and got EV list, removed first one and put it into a new text file
Ran FEAT with melodic switched on, picked components, created a txt file that consisted of colum vectors (TR x noise components)
Ran new FEAT (on original data) that combined all pre-processing steps into one big model, including adding the PNM EV.txt into the voxelwise confound box, adding the ICA txt file into the "add additional confound EVs", adding the first PNM EV as a voxelwise EV in the full model set up (so FEAT would run), and adding my CO2 regressor vector in the full model set up as a "custom 1 entry per volume. (aside: I"m not sure if I need to do the first PNM EV in the full model as I now have the CO2 but that's another story)

So my question is regarding the output:

Liv mentioned I should go into the stats folder and copy the 'res4d.nii.gz' image and rename it as Cleaned_data.

What I want to do is get a functional 4D cleaned image that will have everything I just put into FEAT incorporated, i.e. filtering / bet / smoothing / motion correction / physiological noise correction / ICA artefact correction. Do I add the mean_func image to the residual image? Or combine it with the filtered_func_data somehow?

For example if I wanted to do analyses such as splitting this file in half (as we had a drug infusion in the middle) and subtracting one from the other (to asses the change in BOLD), and then using this to create fALFF maps, what would I need to do to this file (Res4d) first?

(Additionally presumably I would have to register this file to standard space before running group falff analyses?)

If I wanted to run a group MELODIC on these pre-processed FEAT directories, if I used as inputs the lower-level FEATs would they essentially carry through this noise-corrected data?

Apologies for the number of questions, I have searched through a lof of the archive, but still remain unsure..

I really appreciate any advice you can give me!

Anna Forsyth

Anna Forsyth, BA/BSc (Hons), A.T.C.L

PhD Candidate

School of Pharmacy

Faculty of Medical and Health Sciences

University of Auckland