diff --git a/s2b_example_config_EMISEP_long.json b/s2b_example_config_EMISEP_long.json index e22a037..34a0a57 100644 --- a/s2b_example_config_EMISEP_long.json +++ b/s2b_example_config_EMISEP_long.json @@ -1,308 +1,80 @@ { - "study_name": "EMISEP", - "subjects": ["08-74"], - "session": "08-74 MO ENCEPHALE", - "data_to_bids": [ - { - "datasetName": "3D T1 MPRAGE", - "bidsDir": "brain", - "bidsName": "T1w", - "bidsSession": "M00" - }, - { - "datasetName": "*3d flair*", - "bidsDir": "brain", - "bidsName": "FLAIR", - "bidsSession": "M00" - }, - { - "datasetName": "*c1c3*", - "bidsDir": "spinalCord", - "bidsName": "t2ax_C1C3", - "bidsSession": "M00" - }, - { - "datasetName": "*c1-c3*", - "bidsDir": "spinalCord", - "bidsName": "t2ax_C1C3", - "bidsSession": "M00" - }, - { - "datasetName": "*c4c7*", - "bidsDir": "spinalCord", - "bidsName": "t2ax_C4C7", - "bidsSession": "M00" - }, - { - "datasetName": "*c4-c7*", - "bidsDir": "spinalCord", - "bidsName": "t2ax_C4C7", - "bidsSession": "M00" - }, - { - "datasetName": "t2_tse_rr_p2_sag", - "bidsDir": "spinalCord", - "bidsName": "t2Sag", - "bidsSession": "M00" - }, - { - "datasetName": "t2_tse_rr_p2_sag2.5 te 81", - "bidsDir": "spinalCord", - "bidsName": "t2Sag", - "bidsSession": "M00" - }, - { - "datasetName": "t2_tse_sag_384", - "bidsDir": "spinalCord", - "bidsName": "t2Sag", - "bidsSession": "M00" - }, - { - "datasetName": "t2_tse_sag_p2", - "bidsDir": "spinalCord", - "bidsName": "t2Sag", - "bidsSession": "M00" - }, - { - "datasetName": "t2_tse_sag_p2_2mm_te 81 fov 260", - "bidsDir": "spinalCord", - "bidsName": "t2Sag", - "bidsSession": "M00" - }, - { - "datasetName": "SAG T2 CERV", - "bidsDir": "spinalCord", - "bidsName": "t2Sag", - "bidsSession": "M00" - }, - { - "datasetName": "SAG T2 DORSAL", - "bidsDir": "spinalCord", - "bidsName": "t2Sag", - "bidsSession": "M00" - }, - { - "datasetName": "t2_tse_rr_p2_sag2.5 te 81_comp", - "bidsDir": "spinalCord", - "bidsName": "t2Sag-COMP", - "bidsSession": "M00" - }, - { - "datasetName": "t2_tse_rr_p2_sag2.5 te 81_comp_sp", - "bidsDir": "spinalCord", - "bidsName": "t2Sag-COMP", - "bidsSession": "M00" - }, - { - "datasetName": "t2_tse_rr_p2_sag_comp_sp", - "bidsDir": "spinalCord", - "bidsName": "t2Sag-COMP", - "bidsSession": "M00" - }, - { - "datasetName": "t2_tse_sag_384_comp_sp", - "bidsDir": "spinalCord", - "bidsName": "t2Sag-COMP", - "bidsSession": "M00" - }, - { - "datasetName": "t2_tse_sag_p2_2mm_te 81 fov 260_comp_ad", - "bidsDir": "spinalCord", - "bidsName": "t2Sag-COMP", - "bidsSession": "M00" - }, - { - "datasetName": "t2_tse_sag_p2_comp_ad", - "bidsDir": "spinalCord", - "bidsName": "t2Sag-COMP", - "bidsSession": "M00" - }, - { - "datasetName": "SAG T2 TSE MOELLE", - "bidsDir": "spinalCord", - "bidsName": "t2Sag-COMP", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_sag_p2_iso", - "bidsDir": "spinalCord", - "bidsName": "mt0", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_sag_p2_iso mt", - "bidsDir": "spinalCord", - "bidsName": "mt1", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_tra_p2_iso", - "bidsDir": "spinalCord", - "bidsName": "mt0", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_tra_p2_iso mt", - "bidsDir": "spinalCord", - "bidsName": "mt1", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_we_tra_p2_iso", - "bidsDir": "spinalCord", - "bidsName": "mt0", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_we_tra_p2_iso mt tr38", - "bidsDir": "spinalCord", - "bidsName": "mt1", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_we_tra_p2_iso mt tr38 sans sat", - "bidsDir": "spinalCord", - "bidsName": "mt1", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_we_tra_p2_iso mt_tr38 sans sat", - "bidsDir": "spinalCord", - "bidsName": "mt1", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_we_tra_p2_iso tr38", - "bidsDir": "spinalCord", - "bidsName": "mt0", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_we_tra_p2_iso tr38 mt", - "bidsDir": "spinalCord", - "bidsName": "mt1", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_we_tra_p2_iso tr38 mt sans sat", - "bidsDir": "spinalCord", - "bidsName": "mt1", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_we_tra_p2_iso tr38 sans sat", - "bidsDir": "spinalCord", - "bidsName": "mt0", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_we_tra_p2_iso tr38 sans sat_mt", - "bidsDir": "spinalCord", - "bidsName": "mt1", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_we_tra_p2_iso_mt_tr38 sans sat", - "bidsDir": "spinalCord", - "bidsName": "mt1", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_we_tra_p2_iso_mt_tr38_sans_sat", - "bidsDir": "spinalCord", - "bidsName": "mt1", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_we_tra_p2_iso_tr38 sans sat", - "bidsDir": "spinalCord", - "bidsName": "mt0", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_we_tra_p2_m0_iso tr38 sans sat", - "bidsDir": "spinalCord", - "bidsName": "mt0", - "bidsSession": "M00" - }, - { - "datasetName": "t1_fl3d_we_tra_p2_mt_iso tr38", - "bidsDir": "spinalCord", - "bidsName": "mt1", - "bidsSession": "M00" - }, - { - "datasetName": "3d_t1_mprage_sag", - "bidsDir": "spinalCord", - "bidsName": "t1Sag", - "bidsSession": "M00" - }, - { - "datasetName": "t1_mprage_sag_p2_iso", - "bidsDir": "spinalCord", - "bidsName": "t1Sag", - "bidsSession": "M00" - }, - { - "datasetName": "t1_mprage_sag_p2_iso cerv", - "bidsDir": "spinalCord", - "bidsName": "t1Sag", - "bidsSession": "M00" - }, - { - "datasetName": "t1_mprage_sag_p2_iso cerv_rr", - "bidsDir": "spinalCord", - "bidsName": "t1Sag", - "bidsSession": "M00" - }, - { - "datasetName": "t1_mprage_sag_p2_iso ofsep", - "bidsDir": "spinalCord", - "bidsName": "t1Sag", - "bidsSession": "M00" - }, - { - "datasetName": "t1_mprage_sag_p2_iso ofsep_mpr_axial", - "bidsDir": "spinalCord", - "bidsName": "t1Sag", - "bidsSession": "M00" - }, - { - "datasetName": "t1_mprage_sag_p2_iso ofsep_mpr_cor", - "bidsDir": "spinalCord", - "bidsName": "t1Sag", - "bidsSession": "M00" - }, - { - "datasetName": "t1_mprage_sag_p2_iso ofsep_mpr_tra", - "bidsDir": "spinalCord", - "bidsName": "t1Sag", - "bidsSession": "M00" - }, - { - "datasetName": "t1_mprage_sag_p2_iso ofsep_rr", - "bidsDir": "spinalCord", - "bidsName": "t1Sag", - "bidsSession": "M00" - }, - { - "datasetName": "T1 MPRAGE CERV", - "bidsDir": "spinalCord", - "bidsName": "t1Sag", - "bidsSession": "M00" - } - ], - "dcm2niix": "~/softs/miniconda3/bin/dcm2niix", - "dcm2niix_options_comment": "dcm2niix configuration options in the nipype format (see https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.dcm2nii.html)", - "dcm2niix_options": { + "study_name": "EMISEP", + "subjects": ["08-74"], + "session": "08-74 MO ENCEPHALE", + "data_to_bids": + [ + {"datasetName": "3D T1 MPRAGE", "bidsDir": "anat", "bidsName": "T1w", "bidsSession": "M00"}, + {"datasetName": "*3d flair*", "bidsDir": "anat", "bidsName": "FLAIR", "bidsSession": "M00"}, + {"datasetName": "*c1c3*", "bidsDir": "anat", "bidsName": "acq-axC1C3_T2w", "bidsSession": "M00"}, + {"datasetName": "*c1-c3*", "bidsDir": "anat", "bidsName": "acq-axC1C3_T2w", "bidsSession": "M00"}, + + {"datasetName": "*c4c7*", "bidsDir": "anat", "bidsName": "acq-axC4C7_T2w", "bidsSession": "M00"}, + {"datasetName": "*c4-c7*", "bidsDir": "anat", "bidsName": "acq-axC4C7_T2w", "bidsSession": "M00"}, + + + {"datasetName": "t2_tse_rr_p2_sag", "bidsDir": "anat", "bidsName": "acq-sag_T2w", "bidsSession": "M00"}, + {"datasetName": "t2_tse_rr_p2_sag2.5 te 81", "bidsDir": "anat", "bidsName": "acq-sag_T2w", "bidsSession": "M00"}, + {"datasetName": "t2_tse_sag_384", "bidsDir": "anat", "bidsName": "acq-sag_T2w", "bidsSession": "M00"}, + {"datasetName": "t2_tse_sag_p2", "bidsDir": "anat", "bidsName": "acq-sag_T2w", "bidsSession": "M00"}, + {"datasetName": "t2_tse_sag_p2_2mm_te 81 fov 260", "bidsDir": "anat", "bidsName": "acq-sag_T2w", "bidsSession": "M00"}, + {"datasetName": "SAG T2 CERV", "bidsDir": "anat", "bidsName": "acq-sag_T2w", "bidsSession": "M00"}, + {"datasetName": "SAG T2 DORSAL", "bidsDir": "anat", "bidsName": "acq-sag_T2w", "bidsSession": "M00"}, + + {"datasetName": "t2_tse_rr_p2_sag2.5 te 81_comp", "bidsDir": "anat", "bidsName": "acq-sag_rec-COMP_T2w", "bidsSession": "M00"}, + {"datasetName": "t2_tse_rr_p2_sag2.5 te 81_comp_sp", "bidsDir": "anat", "bidsName": "acq-sag_rec-COMP_T2w", "bidsSession": "M00"}, + {"datasetName": "t2_tse_rr_p2_sag_comp_sp", "bidsDir": "anat", "bidsName": "acq-sag_rec-COMP_T2w", "bidsSession": "M00"}, + {"datasetName": "t2_tse_sag_384_comp_sp", "bidsDir": "anat", "bidsName": "acq-sag_rec-COMP_T2w", "bidsSession": "M00"}, + {"datasetName": "t2_tse_sag_p2_2mm_te 81 fov 260_comp_ad", "bidsDir": "anat", "bidsName": "acq-sag_rec-COMP_T2w", "bidsSession": "M00"}, + {"datasetName": "t2_tse_sag_p2_comp_ad", "bidsDir": "anat", "bidsName": "acq-sag_rec-COMP_T2w", "bidsSession": "M00"}, + {"datasetName": "SAG T2 TSE MOELLE", "bidsDir": "anat", "bidsName": "acq-sag_rec-COMP_T2w", "bidsSession": "M00"}, + + + + {"datasetName": "t1_fl3d_sag_p2_iso", "bidsDir": "anat", "bidsName": "mt-off_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_sag_p2_iso mt", "bidsDir": "anat", "bidsName": "mt-on_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_tra_p2_iso", "bidsDir": "anat", "bidsName": "mt-off_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_tra_p2_iso mt", "bidsDir": "anat", "bidsName": "mt-on_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_we_tra_p2_iso", "bidsDir": "anat", "bidsName": "mt-off_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_we_tra_p2_iso mt tr38", "bidsDir": "anat", "bidsName": "mt-on_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_we_tra_p2_iso mt tr38 sans sat", "bidsDir": "anat", "bidsName": "mt-on_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_we_tra_p2_iso mt_tr38 sans sat", "bidsDir": "anat", "bidsName": "mt-on_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_we_tra_p2_iso tr38", "bidsDir": "anat", "bidsName": "mt-off_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_we_tra_p2_iso tr38 mt", "bidsDir": "anat", "bidsName": "mt-on_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_we_tra_p2_iso tr38 mt sans sat", "bidsDir": "anat", "bidsName": "mt-on_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_we_tra_p2_iso tr38 sans sat", "bidsDir": "anat", "bidsName": "mt-off_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_we_tra_p2_iso tr38 sans sat_mt", "bidsDir": "anat", "bidsName": "mt-on_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_we_tra_p2_iso_mt_tr38 sans sat", "bidsDir": "anat", "bidsName": "mt-on_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_we_tra_p2_iso_mt_tr38_sans_sat", "bidsDir": "anat", "bidsName": "mt-on_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_we_tra_p2_iso_tr38 sans sat", "bidsDir": "anat", "bidsName": "mt-off_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_we_tra_p2_m0_iso tr38 sans sat", "bidsDir": "anat", "bidsName": "mt-off_MTR", "bidsSession": "M00"}, + {"datasetName": "t1_fl3d_we_tra_p2_mt_iso tr38", "bidsDir": "anat", "bidsName": "mt-on_MTR", "bidsSession": "M00"}, + + + {"datasetName": "3d_t1_mprage_sag", "bidsDir": "anat", "bidsName": "acq-sag_T1w", "bidsSession": "M00"}, + {"datasetName": "t1_mprage_sag_p2_iso", "bidsDir": "anat", "bidsName": "acq-sag_T1w", "bidsSession": "M00"}, + {"datasetName": "t1_mprage_sag_p2_iso cerv", "bidsDir": "anat", "bidsName": "acq-sag_T1w", "bidsSession": "M00"}, + {"datasetName": "t1_mprage_sag_p2_iso cerv_rr", "bidsDir": "anat", "bidsName": "acq-sag_T1w", "bidsSession": "M00"}, + {"datasetName": "t1_mprage_sag_p2_iso ofsep", "bidsDir": "anat", "bidsName": "acq-sag_T1w", "bidsSession": "M00"}, + {"datasetName": "t1_mprage_sag_p2_iso ofsep_mpr_axial", "bidsDir": "anat", "bidsName": "acq-sag_T1w", "bidsSession": "M00"}, + {"datasetName": "t1_mprage_sag_p2_iso ofsep_mpr_cor", "bidsDir": "anat", "bidsName": "acq-sag_T1w", "bidsSession": "M00"}, + {"datasetName": "t1_mprage_sag_p2_iso ofsep_mpr_tra", "bidsDir": "anat", "bidsName": "acq-sag_T1w", "bidsSession": "M00"}, + {"datasetName": "t1_mprage_sag_p2_iso ofsep_rr", "bidsDir": "anat", "bidsName": "acq-sag_T1w", "bidsSession": "M00"}, + {"datasetName": "T1 MPRAGE CERV", "bidsDir": "anat", "bidsName": "acq-sag_T1w", "bidsSession": "M00"} + + ], + "dcm2niix":"/home/mgaubert/Software/dcm2niix/dcm2niix_v1.0.20211006/dcm2niix", + "dcm2niix_options": { "bids_format": true, - "anon_bids": true, + "anon_bids": false, "compress": "y", "compression": 5, "crop": false, "has_private": false, "ignore_deriv": false, "single_file": false, - "verbose": true + "verbose": false } } + +