CI: add fMRI config for testing FSL FLIRT, global nuisance regression…

…, linear detrending and scrubbing

.circleci/tests/configuration_files/ref_fMRI_config_2.ini

@@ -0,0 +1,72 @@
+[Global]
+process_type = fMRI
+imaging_model = 
+subjects = ['sub-01']
+subject = sub-01
+subject_session = ses-01
+
+[preprocessing_stage]
+discard_n_volumes = 5
+despiking = True
+slice_timing = bottom-top interleaved
+repetition_time = 0.5
+motion_correction = True
+
+[registration_stage]
+ants_convergence_winsize = 10
+ants_nonlinear_update_field_variance = 3.0
+flirt_args =
+contrast_type = dti
+ants_upper_quantile = 0.995
+use_float_precision = False
+ants_nonlinear_total_field_variance = 0.0
+registration_mode = FSL (Linear)
+init = header
+ants_interpolation = Linear
+ants_linear_sampling_perc = 0.25
+apply_to_eroded_wm = True
+ants_convergence_thresh = 1e-06
+ants_multilab_interpolation_parameters = (5.0, 5.0)
+ants_gauss_interpolation_parameters = (5.0, 5.0)
+ants_nonlinear_cost = CC
+ants_bspline_interpolation_parameters = (3,)
+apply_to_eroded_brain = False
+uses_qform = True
+pipeline = fMRI
+ants_lower_quantile = 0.005
+no_search = True
+ants_linear_cost = MI
+ants_linear_gradient_step = 0.1
+apply_to_eroded_csf = True
+ants_perform_syn = True
+ants_linear_sampling_strategy = Regular
+dof = 6
+diffusion_imaging_model =
+fsl_cost = normmi
+ants_nonlinear_gradient_step = 0.1
+
+[functional_stage]
+smoothing = 0.0
+discard_n_volumes = 5
+global_nuisance = True
+csf = True
+wm = True
+motion = True
+detrending = True
+detrending_mode = linear
+lowpass_filter = 0.01
+highpass_filter = 0.1
+scrubbing = True
+
+[connectome_stage]
+output_types = ['gPickle', 'mat']
+apply_scrubbing = True
+fd_thr = 0.2
+dvars_thr = 4.0
+log_visualization = True
+circular_layout = False
+subject = sub-01
+
+[Multi-processing]
+number_of_cores = 1
+