Data Format and Setup Issue

Hi all, 

I am evaluating ReHo using REST for my analysis, and I have a few questions. 

I found this quote in the REST 1.1 English manual: Image file format must be ANALYZE 7.5, and MRIcron or AFNI (Cox, 1996) can be used to transform the format
I used .nii files and it seemed to generate the mReHoMap and the ReHoMap. Are these reliable? Has the code been changed since the publication of the manual incorporating .nii files? 

I have 6 subjects, each with 2 resting state fMRI runs for each subject. I preprocessed using SPM (realign, coreg structural to functional, segment coregistered structural, normalize write using segmentation parameters). I didn't do slice timing correction or smoothing since that would affect ReHo results. I used files with a prefix of 'wr' for REST ReHo analysis. So there were two .nii files for each subject folder, one for each run, with each .nii file being 185 volumes long. I selected each one of the parent folders. I noticed that there is one mReHoMap and ReHoMap for each subject. Will this include the KCC for both the .nii files present in each one of the subject folders? 

Also, I used the NoMask option. Is this an issue? How can I create a user defined mask? I'm sorry if this is a silly question, but I am new to this, hence I ask. 

I took a look at the mReHoMap and the ReHoMap on fslview. I've attached it below. It doesn't look like anything I've seen before. Is this a typical result? 

Finally, I understand that the voxel intensity represents the KCC for the ReHoMap, but what does the mReHoMap mean? The manual says that the mReHoMap is used for 2nd level statistics, but how is it calculated, and what is the range of values for each voxel for this? 

Thank you all for your insight.