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2. List of the MAGIA functions
This page contains both a short list of the most important functions and instructions for their use, as well as a comprehensive list of functions.
run_magia
run_magia is the function that the user calls to trigger analysis of a single study. It acts as an interface between magia_processor and metadata specification. In Turku PET Centre only one input argument, the study ID, is required. Everywhere else also the metadata and the modelling options must be specified.
The metadata must be given as a struct containing the following fields (please use exactly the following names): tracer, frames, use_mri, mri, plasma, rc, dynamic, dc, fwhm, dose and weight.
Also the modelling options must be arranged in a struct. The modelling options struct must always contain the field 'model'. In addition, the struct must contain model-specific fields.
srtm: lb, ub, theta3_lb, theta3_ub, nbases
patlak: start_time, end_frame
patlak_ref: start_time, cut_time, filter_size
fur: start_time, end_time, ic
suvr: start_time, end_time
magia_processor
magia_processor is the main workhorse of the pipeline. It processes a brain PET study with standardized methods. The processing method depends on the tracer, whether the study is dynamic or static, whether an MRI is available for FreeSurfing, and whether plasma input is available for modeling.
The first input argument defines a study id. The function assumes that a folder with exactly the same name exists under getenv('DATA_DIR').
aivo_get_subjects is meant for selecting subjects from AIVO. Examples:
subjects = aivo_get_subjects('tracer','[18f]fdg','analyzed',1);
subjects = aivo_get_subjects('tracer','[11c]raclopride','analyzed',1,'mri','~0');aivo_get_info is meant for reading information from AIVO. Examples:
subjects = aivo_get_subjects('tracer','[18f]fdg','analyzed',1);
weight = aivo_get_info(subjects,'weight');
height = aivo_get_info(subjects,'height');
bmi = weight./((height*0.01)^2);aivo_set_info is meant for writing information to AIVO. Examples:
subjects = aivo_get_subjects('tracer','[18f]fdg','found',1,'mri','~0');
N = length(subjects);
for i = 1:N
sub = subjects{i};
freesurfed = magia_check_freesurfed(sub);
aivo_set_info(sub,'freesurfed',freesurfed);
endaivo_import is meant for creating new subjects to AIVO. The function reads a pre-filled spreadsheet and imports its contents to correct tables in AIVO. Please read this to get more information about how to fill in the metadata.
- aivo_check_found.m
- aivo_connect.m
- aivo_get_info.m
- aivo_get_isotope_from_tracer.m
- aivo_get_subjects.m
- aivo_get_subjects_dev.m
- aivo_parse_me.m
- aivo_read_2tcm_modeling_options.m
- aivo_read_fur_modeling_options.m
- aivo_read_modeling_options.m
- aivo_read_patlak_modeling_options.m
- aivo_read_patlak_ref_modeling_options.m
- aivo_read_srtm_modeling_options.m
- aivo_read_suvr_dyn_modeling_options.m
- aivo_set_info.m
- aivo_set_modeling_options.m
- aivo_store_magia_info.m
- check_megabase_conn.m
- magia_parse_me.m
- magia_metadata_from_aivo.m
- parse_frames_string.m
- get_frame_string.m
- Gunn1997_nifti_mask.m
- PatlakPlasma_nifti.m
- PatlakRef_nifti.m
- calculate_auc_ratio.m
- calculate_fur.m
- calculate_static_ratio.m
- fit_srtm.m
- magia_2tcm_3.m
- magia_calculate_fur_image.m
- simSRTM_1_0_0.m
- roi_fitting.m
- metpet_fit_patlak.m
- metpet_fit_srtm_iterative.m
- magia_fit_2tcm_iterative.m
- magia_fit_patlak_ref.m
- calculate_parametric_images.m
- magia_get_patlak_default_options.m
- magia_get_patlak_ref_default_options.m
- magia_get_2tcm_default_options.m
- magia_get_default_model.m
- magia_get_fur_default_options.m
- magia_suvr_dyn.m
- magia_suvr_dyn_image.m
- magia_suvr_static_image.m
- magia_get_srtm_default_options.m
- magia_get_suvr_dyn_default_options.m
- calculate_fur_integral.m
- metpet_random_init_srtm.m
- magia_archive_results.m
- magia_calculate_input_boundaries.m
- magia_clean_files.m
- magia_combine_seg_and_bs.m
- magia_dev_test.m
- magia_get_githash.m
- magia_get_pet_file.m
- magia_get_ref_region.m
- magia_identify_bad_frames.m
- magia_max_consecutive_values.m
- magia_processor.m
- magia_recon_all.m
- magia_test_dyn.m
- magia_write_githash.m
- magia_write_modeling_options2.m
- run_magia.m
- run_magia_dev.m
- archive_results_new.m
- calculate_input_boundaries.m
- process_mri.m
- decay_correct_to_injection_time.m
- MRIqc.m
- add_to_qc_pic.m
- coreg_qc.m
- input_qc.m
- parametric_image_qc.m
- motion_parameter_qc.m
- mri_histogram_qc.m
- magia_input_qc.m
- smooth_img.m
- spm_coregister_estimate.m
- spm_coregister_reslice.m
- spm_dcm2nii_2.m
- spm_nifti_dynamize.m
- spm_segment.m
- spm_write_4d_nifti.m
- normalize_using_mri.m
- normalize_using_template.m
- motion_correction.m
- roi_bars.m
- visualize_fits.m
- visualize_tacs.m
- plotshaded.m
- shrink_cer.m
- shrink_oc_new.m
- anatomical_reference_region_correction2.m
- data_driven_reference_region_correction_fwhm.m
- magia_check_found.m
- magia_check_freesurfed.m
- magia_check_metadata.m
- magia_check_mri_found.m
- magia_check_plasma_found.m
- magia_check_reversed.m
- convert_ecat2nii.m
- convert_to_nifti.m
- magia_convert_to_nifti.m
- create_brainmask.m
- metpet_fill_brain_img.m
- metpet_fill_line.m
- metpet_fill_slice.m
- read_plasma.m
- read_plasma_dft.m
- metpet_read_plasma_data.m
- add_postfix.m
- add_prefix.m
- get_filenames.m
- center_image.m
- center_image2.m
- cg_set_com_mod.m
- calculate_roi_tacs.m
- create_roi_masks2.m
- create_specific_binding_mask.m
- get_atlas_rois.m
- get_roi_masks.m
- get_tracer_default_roi_set.m
- magia_get_roi_info.m
- remove_nonspecific_binding_from_rois.m
- PSVsmooth_3d.m
- fit_gaussian_mixture.m
- get_ref_tac.m
- get_voxel_time_series.m