ref_anatomical_config.ini
eb6a8acef6d7master

ref_anatomical_config.ini
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			[Global]
			subject_session = ses-01
			subjects = [u'sub-01', u'sub-02']
			process_type = anatomical
			subject = sub-01

			[parcellation_stage]
			parcellation_scheme = Lausanne2018
			brain_file =
			segment_brainstem = True
			thalamic_nuclei_maps = /app/connectomemapper3/cmtklib/data/segmentation/thalamus2018/Thalamus_Nuclei-HCP-4DSPAMs.nii.gz
			include_thalamic_nuclei_parcellation = True
			template_thalamus = /app/connectomemapper3/cmtklib/data/segmentation/thalamus2018/mni_icbm152_t1_tal_nlin_sym_09b_hires_1.nii.gz
			pre_custom = Lausanne2008
			atlas_nifti_file =
			parcellation_scheme_editor = ['NativeFreesurfer', 'Lausanne2008', 'Lausanne2018', 'Custom']
			number_of_regions = 0
			segment_hippocampal_subfields = True
			graphml_file =
			atlas_info = {}
			pipeline_mode = Diffusion
			csf_file =

			[segmentation_stage]
			make_isotropic = True
			freesurfer_subject_id =
			isotropic_interpolation = cubic
			isotropic_vox_size = 1.0
			freesurfer_subjects_dir =
			ants_templatefile = /app/connectomemapper3/cmtklib/data/segmentation/ants_template_IXI/T_template2_BrainCerebellum.nii.gz
			freesurfer_args =
			brain_mask_extraction_tool = Freesurfer
			white_matter_mask =
			ants_regmaskfile = /app/connectomemapper3/cmtklib/data/segmentation/ants_template_IXI/T_template_BrainCerebellumMask.nii.gz
			seg_tool = Freesurfer
			use_fsl_brain_mask = False
			brain_mask_path =
			ants_probmaskfile = /app/connectomemapper3/cmtklib/data/segmentation/ants_template_IXI/T_template_BrainCerebellumProbabilityMask.nii.gz
			use_existing_freesurfer_data = False

			[Multi-processing]
			number_of_cores = 1