Dear FSL Experts,
I have some questions using Melodic and I would appreciate if you could help me with them. Thanks in advance
1. If I have several runs for each subject and I want to do multi-session temporal concatenation , should I concatenate the runs of each subject using fslmerge and then give it as a single subject data to Melodic or I should just give all the runs of all subjects as 4D input data. Is there any point for one method to be better than the other in terms of preprocessing steps (intensity/motion) and ICA step (application/reconstruction)?
2. Considering that what I am doing is to feed fsl, n times (n=number of runs for one subject) and then doing concatenated temporal ICA on these n images. My question is whether or not the result would be different if I first concatenate all runs into one image and finally apply a single session ICA on it?
3. I suppose the motion correction step in preprocessing is just to do motion correction within the runs. But what happens when you have multiple runs of one subject? I mean if I decide to concatenate several runs of one subject what should I do? Do I need to do the intensity normalization, smoothing and sinc interpolation before? I did the simplest form of concatenation but when you move from the last volume of one run to the first volume of the other one there is a shift in intensity (or may be it is some movement).
4. My primary data was in minc format and I changed it to nii format. The z steps in mnc file were negative and the image had neurological convention. The nii images have positive steps and I am not sure if they have neurological or radiological convention. I suppose they are still in neurological convention since I have left-to-right in sform_orient. So before using mnc files to do slice timing correction my choice was regular down but I am a bit confused about nii files. Should it be regular up now considering the positive steps?