remove parfor from spatial processing and add QA options

[Remi-Gau]

fixes #389

@CerenB and @marcobarilari I have added some options for functional QA that should speed it up and prevent generating some (big) files.

opt.QA.func.carpetPlot = true to plot carpet plot when running functionaQA

opt.QA.func contains a lot of options used by spmup_first_level_qa in functionaQA
opt.QA.func.MotionParameters = 'on'
opt.QA.func.FramewiseDisplacement = 'on'
opt.QA.func.Voltera = 'on'
opt.QA.func.Globals = 'on'
opt.QA.func.Movie = 'on' ; set it to off to skip generating movies of the time series
opt.QA.func.Basics = 'on'

@marcobarilari I have changed the name of the option to skip the GLM QA that sometimes took ages for you:
opt.QA.glm.do = true.

[CerenB]

working on my local! A slight hiccup is when I ran the following, I got an orientation dimension mismatch error. Maybe I'm not updated with the latest changes on how to run functionalQA ?

What works:

% % Quality control
anatomicalQA(opt);
bidsResliceTpmToFunc(opt);

When crashes:
functionalQA(opt);

Error is below:

FOR TASK: auditoryLocalizer
WILL WORK ON SUBJECTS
    '009'

 FUNCTIONAL: QUALITY CONTROL

 PROCESSING SUBJECT No.: 1 SUBJECT ID : 009 

    ** The images do not all have the same dimensions. **
The function assumes that a voxel in one image corresponds with
the same  voxel in another.   This  is not a safe assumption if
the  image dimensions differ.   Please  ensure  that  you  have
processed all the image data in the same way (eg. check spatial
normalisation bounding-boxes, voxel-sizes etc).
Here are the dimensions of the image volumes.  This list can be
used to determine which file(s) are causing the problem.

[84 84 58]  /Users/battal/Cerens_files/fMRI/Processed/MT_TMS/derivatives/cpp_spm/sub-009/ses-001/func/uasub-009_ses-001_task-auditoryLocalizer_run-001_bold.nii
[84 84 58]  /Users/battal/Cerens_files/fMRI/Processed/MT_TMS/derivatives/cpp_spm/sub-009/ses-001/func/uasub-009_ses-001_task-auditoryLocalizer_run-001_bold.nii
...
[84 84 58]  /Users/battal/Cerens_files/fMRI/Processed/MT_TMS/derivatives/cpp_spm/sub-009/ses-001/func/uasub-009_ses-
[61 73 61]  /Users/battal/Cerens_files/fMRI/Processed/MT_TMS/derivatives/cpp_spm/sub-009/ses-001/anat/rc1sub-009_ses-001_T1w.nii
[61 73 61]  /Users/battal/Cerens_files/fMRI/Processed/MT_TMS/derivatives/cpp_spm/sub-009/ses-001/anat/rc2sub-009_ses-001_T1w.nii
[61 73 61]  /Users/battal/Cerens_files/fMRI/Processed/MT_TMS/derivatives/cpp_spm/sub-009/ses-001/anat/rc3sub-009_ses-001_T1w.nii

Error using spm_check_orientations (line
42)
The dimensions must be identical for
this procedure.

Error in functionalQA (line 80)
        spm_check_orientations(spm_vol(char(volumesToCheck))); 

[CerenB]

oh maybe one more name changing is needed. Please see below:

Reference to non-existent field 'QA'.

Error in
setBatchEstimateModel>returnEstimateModelBatch
(line 62)
  if ~opt.glm.QA.do

Error in setBatchEstimateModel (line 32)
      matlabbatch =
      returnEstimateModelBatch(matlabbatch,
      spmMatFile, opt);

Error in bidsFFX (line 73)
        matlabbatch =
        setBatchEstimateModel(matlabbatch,
        opt);

[Remi-Gau]

working on my local! A slight hiccup is when I ran the following, I got an orientation dimension mismatch error. Maybe I'm not updated with the latest changes on how to run functionalQA ?

it seems that you did reslice the TPMs before doing the functional QA but that the resolution is not right.

that could be the issue.

Do you run those 2 in sequence?

bidsResliceTpmToFunc(opt);
functionalQA(opt)

[Remi-Gau]

@CerenB will merge this for now but let me know if you get this bug again.