So I had a few questions in regards using the FATCAT toolbox. I
So a little background… Basically, I’m trying to combine resting state fmri with dti (copying the example given in the FATCAT paper but with my own data).
So first off, in the example given in the paper. Spatial ICA is used in native functional space with FSL-melodic.
First question I have from this is how to run spatial ICA? I read many documents to make sense of this. There are some papers that claim you can run ICA either in sICA (spatial ICA) or tICA (temporal ICA). But there are no settings in MELODIC that distinctly distinguishes the two? I have come across a paper however that discusses when working with rs-fmri data it is useful to apply sICA because of the resting-state networks are not consistent temporally. So it was advised to concatenate all subjects data temporally first (by running a group PCA reduction on each subject, then concatenate it, and lastly perform a PCA reduction on the concatenated work). Once PCA is performed, one can run ICA, and after a backward reconstruction? Also, how would I do this using a code?
Another method I read online was to download a toolbox: GIFT (Group ICA of fMRI Toolbox) which is a toolbox that works on MATLAB that apparently does all the group independent component analysis with PCA and all, automatically.
Lastly, I’ve also come across a document that used MELODIC for group ICA (multi-session temporal concatenation).
p.s. I’m aware that there is ICA done by averaging all the subjects and then there’s the one where you study each individual subject on its own (the ICA) and can perform in within group and between group study using a t-test?
So my question is: which method is more accurate? Maybe it’s a bit of information overload but now it seems that there are many options and no clear path of what to do.
My next question is when it claims that has to do with the mention of using sICA in native functional space. Does that mean that it wasn’t registered onto standard space? So in MELODIC, under the registration tab, was ONLY the structural image and functional image entered? And not the standard space? And if so, why would that be the case? Also, in the example given in the FATCAT paper, rs-fmri and DTI were combined. However, wasn’t the fMRI image supposed to be transformed to DWI space? And if so, how can I do that? From what I understand, is that fMRI images are supposed to be translated to standard space, then translated into DWI data? I’m a little confused about this, and the concept of having to translate into different spaces?
Last question I have is how do I obtain the z-score? I noticed MELODIC only outputs the z-threshold? Many papers report the z-score, so I’m wondering how to obtain that value with the given output from MELODIC.
Any help would be greatly appreciate it. I apologize for the lengthy question. Hope to hear from you soon .