Allow separate B1 map for MTsat B1 correction

[lukeje]

The B1 inhomogeneities of the excitation pulses and the MT pulse can be different, especially if pTx is used, meaning that they will need different B1 maps for correction. This pull request changes the user interface to allow two B1 maps to be provided, one to correct the excitation pulses (for R1 and PD calculation) and one to correct the MT pulses (for the MTsat calculation).

Some considerations:

• Not clear if compatible with UNICORT
• Will break any old batch files, as it adds an extra selection layer for the B1 map data
• Not clear if compatible with Helms MTsat correction model

Edit: Followed Baris' suggestion to not break old batch files, and I think UNICORT should work fine as long as a different B1 map is provided for the MT pulse.

Edit2: Followed Gunther's suggestion on how to undo implicit B1 correction when using the Helms model and a separate MT pulse B1 map.

[Barisevrenugur]

it looks like on this line (in the conditional) you are setting f_T_MT to its correct value (f_T or etc.) for the rest of the MTprot:

hMRI-toolbox/hmri_create_MTProt.m

Line 858 in 9ccbe0f

f_T_MT = f_T;

but then I would expect only f_T_MT from the above conditional onward but you still have f_T s lurking around for instance on these lines:

hMRI-toolbox/hmri_create_MTProt.m

Line 878 in 9ccbe0f

if (~isempty(f_T))&&(~mpm_params.UNICORT.R1 || mpm_params.UNICORT.MT)

hMRI-toolbox/hmri_create_MTProt.m

Line 1078 in 9ccbe0f

if ~isempty(f_T) && ~isempty(fA) && exist('fTPM','var') && (mpm_params.UNICORT.PD || ~mpm_params.UNICORT.R1)

That would be great if you can look at those lines again and confirm those are not some sort of artifact from merging the master into this one or a bug. Thanks in advance.

[lukeje]

Good catch; yes these look like lines from the error maps branch which weren't in the ancestor and so weren't updated... I'll fix them.

[lukeje]

Ah, wait. Only the f_T inside the MTsat calculation conditional needs to be corrected. The other is about correcting PD which was computed with the original f_T. I'll push the fix now.

[Barisevrenugur]

I just corrected another bug:
68e04fb

this was the bug:

	-------- Map calculation continued (MT, A/PD) --------
26-Feb-2025 18:15:21 - Failed  'Create hMRI maps'
Unrecognized function or variable 'dMTsatcorr'.
In file "/data/u_ugurcan_software/gitreps-test/rep-1/hMRI-toolbox/hmri_create_MTProt.m" (???), function "hmri_create_MTProt" at line 880.
In file "/data/u_ugurcan_software/gitreps-test/rep-1/hMRI-toolbox/hmri_run_create.m" (???), function "hmri_create_local" at line 158.
In file "/data/u_ugurcan_software/gitreps-test/rep-1/hMRI-toolbox/hmri_run_create.m" (???), function "hmri_run_create" at line 24.

The following modules did not run:
Failed: Create hMRI maps