REL: Connectome Mapper Release v3.0.0

.circleci/tests/configuration_files/ref_anatomical_config_1.ini

@@ -6,7 +6,7 @@ subject = sub-01
 
 [segmentation_stage]
 ants_templatefile = 
-make_isotropic = True
+make_isotropic = False
 freesurfer_subject_id = 
 isotropic_interpolation = cubic
 isotropic_vox_size = 1.0
@@ -25,19 +25,19 @@ number_of_threads = 2
 [parcellation_stage]
 parcellation_scheme = Lausanne2018
 brain_file = 
-segment_hippocampal_subfields = True
-segment_brainstem = True
+segment_hippocampal_subfields = False
+segment_brainstem = False
 ants_precision_type = float
 thalamic_nuclei_maps = app/connectomemapper3/cmtklib/data/segmentation/thalamus2018/Thalamus_Nuclei-HCP-4DSPAMs.nii.gz
-include_thalamic_nuclei_parcellation = True
+include_thalamic_nuclei_parcellation = False
 template_thalamus = app/connectomemapper3/cmtklib/data/segmentation/thalamus2018/mni_icbm152_t1_tal_nlin_sym_09b_hires_1.nii.gz
 pipeline_mode = Diffusion
 atlas_nifti_file = 
-parcellation_scheme_editor = ['NativeFreesurfer', 'Lausanne2008', 'Lausanne2018', 'Custom']
+parcellation_scheme_editor = ['NativeFreesurfer', 'Lausanne2018', 'Custom']
 number_of_regions = 0
 graphml_file = 
 atlas_info = {}
-pre_custom = Lausanne2008
+pre_custom = Lausanne2018
 csf_file = 
 
 [Multi-processing]

.circleci/tests/configuration_files/ref_anatomical_config_2.ini

@@ -6,7 +6,7 @@ subject = sub-01
 
 [segmentation_stage]
 ants_templatefile =
-make_isotropic = True
+make_isotropic = False
 freesurfer_subject_id =
 isotropic_interpolation = cubic
 isotropic_vox_size = 1.0
@@ -33,11 +33,11 @@ include_thalamic_nuclei_parcellation = True
 template_thalamus = app/connectomemapper3/cmtklib/data/segmentation/thalamus2018/mni_icbm152_t1_tal_nlin_sym_09b_hires_1.nii.gz
 pipeline_mode = Diffusion
 atlas_nifti_file =
-parcellation_scheme_editor = ['NativeFreesurfer', 'Lausanne2008', 'Lausanne2018', 'Custom']
+parcellation_scheme_editor = ['NativeFreesurfer', 'Lausanne2018', 'Custom']
 number_of_regions = 0
 graphml_file =
 atlas_info = {}
-pre_custom = Lausanne2008
+pre_custom = Lausanne2018
 csf_file =
 
 [Multi-processing]

.circleci/tests/configuration_files/ref_anatomical_config_3.ini

@@ -6,7 +6,7 @@ subject = sub-01
 
 [segmentation_stage]
 ants_templatefile = 
-make_isotropic = True
+make_isotropic = False
 freesurfer_subject_id = 
 isotropic_interpolation = cubic
 isotropic_vox_size = 1.0
@@ -23,7 +23,7 @@ use_existing_freesurfer_data = False
 number_of_threads = 2
 
 [parcellation_stage]
-parcellation_scheme = Lausanne2008
+parcellation_scheme = Custom
 brain_file = 
 segment_hippocampal_subfields = True
 segment_brainstem = True
@@ -33,11 +33,11 @@ include_thalamic_nuclei_parcellation = True
 template_thalamus = app/connectomemapper3/cmtklib/data/segmentation/thalamus2018/mni_icbm152_t1_tal_nlin_sym_09b_hires_1.nii.gz
 pipeline_mode = Diffusion
 atlas_nifti_file = 
-parcellation_scheme_editor = ['NativeFreesurfer', 'Lausanne2008', 'Lausanne2018', 'Custom']
+parcellation_scheme_editor = ['NativeFreesurfer', 'Lausanne2018', 'Custom']
 number_of_regions = 0
 graphml_file = 
 atlas_info = {}
-pre_custom = Lausanne2008
+pre_custom = Lausanne2018
 csf_file = 
 
 [Multi-processing]

.circleci/tests/configuration_files/ref_anatomical_config_3.json

@@ -0,0 +1,45 @@
+{
+    "Global": {
+        "process_type": "anatomical",
+        "subjects": [
+            "sub-01"
+        ],
+        "subject": "sub-01",
+        "subject_session": "ses-01",
+        "version": "v3.0.0"
+    },
+    "segmentation_stage": {
+        "seg_tool": "Custom segmentation",
+        "custom_brainmask.toolbox_derivatives_dir": "cmp-custom",
+        "custom_brainmask.suffix": "mask",
+        "custom_brainmask.extension": "nii.gz",
+        "custom_brainmask.desc": "brain",
+        "custom_wm_mask.toolbox_derivatives_dir": "cmp-custom",
+        "custom_wm_mask.suffix": "dseg",
+        "custom_wm_mask.extension": "nii.gz",
+        "custom_wm_mask.label": "WM",
+        "custom_gm_mask.toolbox_derivatives_dir": "cmp-custom",
+        "custom_gm_mask.suffix": "dseg",
+        "custom_gm_mask.extension": "nii.gz",
+        "custom_gm_mask.label": "GM",
+        "custom_csf_mask.toolbox_derivatives_dir": "cmp-custom",
+        "custom_csf_mask.suffix": "dseg",
+        "custom_csf_mask.extension": "nii.gz",
+        "custom_csf_mask.label": "CSF",
+        "custom_aparcaseg.toolbox_derivatives_dir": "cmp-custom",
+        "custom_aparcaseg.suffix": "dseg",
+        "custom_aparcaseg.extension": "nii.gz",
+        "custom_aparcaseg.desc": "aparcaseg"
+    },
+    "parcellation_stage": {
+        "parcellation_scheme": "Custom",
+        "custom_parcellation.toolbox_derivatives_dir": "cmp-custom",
+        "custom_parcellation.suffix": "dseg",
+        "custom_parcellation.res": "scale1",
+        "custom_parcellation.extension": "nii.gz",
+        "custom_parcellation.atlas": "L2018"
+    },
+    "Multi-processing": {
+        "number_of_cores": 1
+    }
+}

.circleci/tests/configuration_files/ref_diffusion_config_1.ini

@@ -11,7 +11,7 @@ tracking_processing_tool_editor = ['Dipy', 'MRtrix', 'Custom']
 tracking_processing_tool = MRtrix
 dilation_kernel = Box
 recon_processing_tool_editor = ['Dipy', 'Custom']
-custom_track_file = 
+custom_track_file =
 dilation_radius = 1
 diffusion_model = Deterministic
 dilate_rois = True
@@ -89,7 +89,7 @@ denoising_algo = MRtrix (MP-PCA)
 bias_field_algo = ANTS N4
 bias_field_correction = True
 fast_use_priors = True
-resampling = (2, 2, 2)
+resampling = (3, 3, 3)
 partial_volume_estimation = True
 eddy_correction_algo = FSL eddy_correct
 interpolation = interpolate
@@ -100,12 +100,12 @@ output_types = ['gPickle', 'mat', 'graphml']
 compute_curvature = True
 log_visualization = True
 connectivity_metrics = ['Fiber number', 'Fiber length', 'Fiber density', 'Fiber proportion', 'Normalized fiber density', 'ADC', 'gFA']
-subject = 
+subject =
 
 [registration_stage]
 pipeline = Diffusion
-registration_mode = FSL
-diffusion_imaging_model = 
+registration_mode = FSL (Linear)
+diffusion_imaging_model =
 use_float_precision = False
 ants_interpolation = BSpline
 ants_bspline_interpolation_parameters = (3,)
@@ -124,7 +124,7 @@ ants_nonlinear_gradient_step = 0.1
 ants_nonlinear_cost = CC
 ants_nonlinear_update_field_variance = 3.0
 ants_nonlinear_total_field_variance = 0.0
-flirt_args = 
+flirt_args =
 uses_qform = True
 dof = 6
 fsl_cost = normmi

.circleci/tests/configuration_files/ref_diffusion_config_2.ini

@@ -11,7 +11,7 @@ tracking_processing_tool_editor = ['Dipy', 'MRtrix', 'Custom']
 tracking_processing_tool = MRtrix
 dilation_kernel = Box
 recon_processing_tool_editor = ['Dipy', 'Custom']
-custom_track_file = 
+custom_track_file =
 dilation_radius = 1
 diffusion_model = Probabilistic
 dilate_rois = True
@@ -89,7 +89,7 @@ denoising_algo = MRtrix (MP-PCA)
 bias_field_algo = ANTS N4
 bias_field_correction = True
 fast_use_priors = True
-resampling = (2, 2, 2)
+resampling = (3, 3, 3)
 partial_volume_estimation = True
 eddy_correction_algo = FSL eddy_correct
 interpolation = interpolate
@@ -100,12 +100,12 @@ output_types = ['gPickle']
 compute_curvature = False
 log_visualization = True
 connectivity_metrics = ['Fiber number', 'Fiber length', 'Fiber density', 'Fiber proportion', 'Normalized fiber density', 'ADC', 'gFA']
-subject = 
+subject =
 
 [registration_stage]
 ants_convergence_winsize = 10
 ants_nonlinear_update_field_variance = 3.0
-flirt_args = 
+flirt_args =
 contrast_type = dti
 ants_upper_quantile = 0.995
 use_float_precision = False
@@ -131,7 +131,7 @@ apply_to_eroded_csf = True
 ants_perform_syn = True
 ants_linear_sampling_strategy = Regular
 dof = 6
-diffusion_imaging_model = 
+diffusion_imaging_model =
 fsl_cost = normmi
 ants_nonlinear_gradient_step = 0.1
 

.circleci/tests/configuration_files/ref_diffusion_config_3.ini

@@ -88,7 +88,7 @@ denoising_algo = MRtrix (MP-PCA)
 bias_field_algo = ANTS N4
 bias_field_correction = True
 fast_use_priors = True
-resampling = (2, 2, 2)
+resampling = (3, 3, 3)
 partial_volume_estimation = True
 eddy_correction_algo = FSL eddy_correct
 interpolation = interpolate

.circleci/tests/configuration_files/ref_diffusion_config_4.ini

@@ -88,7 +88,7 @@ denoising_algo = MRtrix (MP-PCA)
 bias_field_algo = ANTS N4
 bias_field_correction = True
 fast_use_priors = True
-resampling = (2, 2, 2)
+resampling = (3, 3, 3)
 partial_volume_estimation = True
 eddy_correction_algo = FSL eddy_correct
 interpolation = interpolate

.circleci/tests/configuration_files/ref_diffusion_config_5.ini

@@ -19,7 +19,7 @@ eddy_correction_algo = FSL eddy_correct
 eddy_correct_motion_correction = True
 partial_volume_estimation = True
 fast_use_priors = True
-resampling = (1, 1, 1)
+resampling = (3, 3, 3)
 interpolation = interpolate
 
 [registration_stage]