update SingleSubjectConcat with frame selection; update MSMAll pipeline

[cyang31]

This is the squash and merge version of a previous PR

Background

Previously the script SingleSubjectConcat.sh doesn't enable the frame range selection for each fMRI runs. Hence, the MSMAll is limited to be only applied to the full timeseries.

Main changes

• replace the old opt with Tim's newopt library in SingleSubjectConcat.sh;
• remove the bias correction and computation of VN files in SingleSubjectConcat.sh;
• add two optional arguments StartFrame and EndFrame in SingleSubjectConcat.sh and MSMAllPipeline.sh;
• validate the input frame range and throw an error if invalid range is provided in SingleSubjectConcat.sh;

Evaluation

One subject with resting state fMRI is evaluated. No error.

[glasserm]

I forget, is this fully tested? If so we might just merge this one.

[cyang31]

I forget, is this fully tested? If so we might just merge this one.
Yes, it has been fully tested.

[coalsont]

Let's use the original one, so we don't need to compare whether this one has completely identical changes.