Name		Name	Last commit message	Last commit date
Latest commit History 465 Commits
aivo		aivo
examples		examples
templates		templates
.gitignore		.gitignore
Gunn1997_nifti_mask.m		Gunn1997_nifti_mask.m
LICENSE		LICENSE
MRIqc.m		MRIqc.m
README.md		README.md
add_postfix.m		add_postfix.m
add_prefix.m		add_prefix.m
add_to_qc_pic.m		add_to_qc_pic.m
anatomical_reference_region_correction2.m		anatomical_reference_region_correction2.m
calculate_fur_integral.m		calculate_fur_integral.m
calculate_input_boundaries.m		calculate_input_boundaries.m
center_image.m		center_image.m
cg_set_com_mod.m		cg_set_com_mod.m
convert_ecat2nii.m		convert_ecat2nii.m
convert_to_nifti.m		convert_to_nifti.m
coreg_qc.m		coreg_qc.m
create_roi_masks2.m		create_roi_masks2.m
create_specific_binding_mask.m		create_specific_binding_mask.m
data_driven_reference_region_correction_fwhm.m		data_driven_reference_region_correction_fwhm.m
decay_correct_to_injection_time.m		decay_correct_to_injection_time.m
fit_srtm.m		fit_srtm.m
force_ras.m		force_ras.m
get_filenames.m		get_filenames.m
get_frame_string.m		get_frame_string.m
get_half_life.m		get_half_life.m
get_ref_tac.m		get_ref_tac.m
input_qc.m		input_qc.m
magia_2tcm_3.m		magia_2tcm_3.m
magia_archive_results.m		magia_archive_results.m
magia_calc_roi_volume.m		magia_calc_roi_volume.m
magia_calculate_fur.m		magia_calculate_fur.m
magia_calculate_fur_image.m		magia_calculate_fur_image.m
magia_calculate_input_boundaries.m		magia_calculate_input_boundaries.m
magia_calculate_roi_tacs.m		magia_calculate_roi_tacs.m
magia_center_image.m		magia_center_image.m
magia_check_envs.m		magia_check_envs.m
magia_check_found.m		magia_check_found.m
magia_check_found_mri.m		magia_check_found_mri.m
magia_check_freesurfed.m		magia_check_freesurfed.m
magia_check_metadata.m		magia_check_metadata.m
magia_check_mri_found.m		magia_check_mri_found.m
magia_check_reversed.m		magia_check_reversed.m
magia_check_specs.m		magia_check_specs.m
magia_clean_files.m		magia_clean_files.m
magia_clean_specs.m		magia_clean_specs.m
magia_combine_seg_and_bs.m		magia_combine_seg_and_bs.m
magia_convert_ki_to_gu.m		magia_convert_ki_to_gu.m
magia_convert_ki_to_gu_img.m		magia_convert_ki_to_gu_img.m
magia_convert_to_nifti.m		magia_convert_to_nifti.m
magia_correct_refinput.m		magia_correct_refinput.m
magia_correct_rois.m		magia_correct_rois.m
magia_create_brainmask.m		magia_create_brainmask.m
magia_create_fs_ref_mask.m		magia_create_fs_ref_mask.m
magia_fit_2tcm_iterative.m		magia_fit_2tcm_iterative.m
magia_fit_logan.m		magia_fit_logan.m
magia_fit_logan_ref.m		magia_fit_logan_ref.m
magia_fit_ma1.m		magia_fit_ma1.m
magia_fit_patlak.m		magia_fit_patlak.m
magia_fit_patlak_ref.m		magia_fit_patlak_ref.m
magia_fix_first_frame.m		magia_fix_first_frame.m
magia_get_2tcm_default_options.m		magia_get_2tcm_default_options.m
magia_get_default_model.m		magia_get_default_model.m
magia_get_default_specs.m		magia_get_default_specs.m
magia_get_freesurfer_roi_info.m		magia_get_freesurfer_roi_info.m
magia_get_fur_default_options.m		magia_get_fur_default_options.m
magia_get_githash.m		magia_get_githash.m
magia_get_input.m		magia_get_input.m
magia_get_logan_default_options.m		magia_get_logan_default_options.m
magia_get_logan_ref_default_options.m		magia_get_logan_ref_default_options.m
magia_get_ma1_default_options.m		magia_get_ma1_default_options.m
magia_get_mri_file.m		magia_get_mri_file.m
magia_get_patlak_default_options.m		magia_get_patlak_default_options.m
magia_get_patlak_ref_default_options.m		magia_get_patlak_ref_default_options.m
magia_get_pet_file.m		magia_get_pet_file.m
magia_get_ref_mask.m		magia_get_ref_mask.m
magia_get_ref_region.m		magia_get_ref_region.m
magia_get_srtm_default_options.m		magia_get_srtm_default_options.m
magia_get_suvr_default_options.m		magia_get_suvr_default_options.m
magia_get_tracer_default_roi_set.m		magia_get_tracer_default_roi_set.m
magia_identify_bad_frames.m		magia_identify_bad_frames.m
magia_input_qc.m		magia_input_qc.m
magia_logan_image.m		magia_logan_image.m
magia_logan_ref_image.m		magia_logan_ref_image.m
magia_ma1_image.m		magia_ma1_image.m
magia_match_input_to_model.m		magia_match_input_to_model.m
magia_match_units.m		magia_match_units.m
magia_max_consecutive_values.m		magia_max_consecutive_values.m
magia_medfilter.m		magia_medfilter.m
magia_medfilter_slice.m		magia_medfilter_slice.m
magia_motion_correction.m		magia_motion_correction.m
magia_parse_excluded_frames.m		magia_parse_excluded_frames.m
magia_patlak_image.m		magia_patlak_image.m
magia_patlak_ref_image.m		magia_patlak_ref_image.m
magia_processor.m		magia_processor.m
magia_read_input.m		magia_read_input.m
magia_read_specs.m		magia_read_specs.m
magia_recon_all.m		magia_recon_all.m

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Magia

Magia is an automated processing pipeline for brain PET studies. Magia uses FreeSurfer to parcellate the brain into anatomical regions of interest, and performs kinetic modeling using tools developed over the years at Turku PET Center.

Magia has been shown to generate reference regions that yield results similar to results derived using manually delineated reference regions (Karjalainen et al. 2020, https://doi.org/10.3389/fninf.2020.00003). Please cite the paper if you use Magia.

Please see the wiki page (https://github.com/tkkarjal/magia/wiki) for installation and usage instructions.

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tkkarjal/magia

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