I am relatively new to resting state analysis and the DPARSFA toolbox, any comments, suggestions and feedback to the following questions would be highly appreciated!
Has someone worked with fieldmaps in SPM, realigned & unwarped in SPM and then continued the preprocessing and FC analysis in DPARSFA? If so, what are the options required to be checked in DPARSFA to continue the preprocessing? I'd like to get some advice on how you organised your workflow (i.e. your pre-processing steps).
I have resting state data (2 runs/person) and field map information. I discovered that there were substantial field inhomogeneities which I needed to correct for using subjects' field maps. DPARSFA cannot (at present) incorporate this step into the preprocessing, which is why I have used the Fieldmap toolbox in SPM8 to generate vdm files, and have used these to realign & unwarp my data. (It seems not possible to only unwarp in SPM, hence I also had to realign outside of DPARSFA.) I would now like to use the realigned, unwarped images for the rest of the preprocessing and functional connectivity analysis in DPARSFA, but am unsure which options to check for preprocessing given that my images are already realigned & unwarped.
Can I leave out the realign option in DPARSFA and still obtain valid results after analysis? It appears that, when I leave realign unchecked but check all other options, the code crashes during the next step. During the last step of preprocessing, covariates are regressed out. With realign being left unchecked, no motion parameters are being regressed out, only CSF and WM (if ticked). Is it true that, because of the unwarping step, motion parameters do not need to be regressed out during the last step of preprocessing?
Apologies for the long query, as I said I am new to this and am still learning. Any advice would be greatly appreciated!