Enable different set of bolds for each session in TransmitLong

[sivcek]

Currently TransmitBiasLong assumes that all the sessions have the exact same set of fMRI images. This often is not the case in longitudinal datasets. This PR enables specifying different set of fMRI images for each session while keeping backward compatibility with old behavior. If a user desires to specify different set of fMRI images for each session, they list fMRI names for each session in the --pt-fmri-names argument, separating sessions with % character. If no % character is present, the same set of fMRI names is used for all sessions. If % character is present, the code checks whether the number of fMRI sets match the number of sessions, and uses the sets in the same order as the sessions are listed.

In the example:

--sessions="session1@session2@session2" \
--pt-fmri-names="rest@taskA@taskB%rest@taskA%rest@taskB"

the pairings are:

• session1 – rest, taskA, and taskB,
• session2 – rest, taskA
• session3 – rest, taskB

[glasserm]

This looks fine to me.

[mharms]

Just an observation that my initial thought is that we'd want to use @ in this type of situation to consistently represent the delimiter between sessions (as used in --sessions), and then introduce the 2nd delimiter to distinguish the different fMRI runs within a session, e.g.
--pt-fmri-names="rest%taskA%taskB@rest%taskA@rest%taskB"
but I see that @sivcek's implementation is consistent with how we treat the addition of a 2nd delimiter in DeDriftAndResamplePipeline.sh

So, the heuristic that we've adopted instead is that @ is always the innermost delimiter, even if that means it delimits sessions in one flag, but runs in a different flag within the same script.

[mharms]

Suggested change

	opts_AddOptional '--pt-fmri-names' 'fMRINames' 'rfMRI_REST1_LR@rfMRI_REST1_RL...' "fmri runs to use SE/SBRef files from, separated by @. For per-session lists, separate session-specific sets using % (e.g., run1@run2%run2%run1@run3)."
	opts_AddOptional '--pt-fmri-names' 'fMRINames' 'rfMRI_REST1_LR@rfMRI_REST1_RL...' "fmri runs to use SE/SBRef files from, separated by @. For per-session lists, separate session-specific sets using % (e.g., run1@run2%run2%run1@run3 to use run1 and run2 from session1, run2 from session2, and run1 and run3 from session3)."

[mharms]

Suggested a bit more wording to make the example very explicit.

[glasserm]

@sivcek @coalsont @mharms can we get this merged?

[mharms]

Looks like we are waiting for @sivcek to respond to my earlier suggestion, and for @coalsont to chime in...

[coalsont]

Looks reasonable to me.