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Bids 1.9.0 spinal cord #17

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Bids 1.9.0 spinal cord #17

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bcc71c8
added BIDS modifications for spinal cord
alexpron Apr 16, 2024
1f33c9d
added BIDS modifications for spinal cord
alexpron Apr 16, 2024
ec6f0f6
Merge remote-tracking branch 'origin/bids-1.9.0-spinal-cord' into bid…
alexpron Jul 25, 2024
e71273c
[BF+ ENH]: added dcm2niix_options in nipype format and correct bidsdi…
alexpron Jul 25, 2024
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368 changes: 70 additions & 298 deletions s2b_example_config_EMISEP_long.json
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Original file line number Diff line number Diff line change
@@ -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
}
}