TEST_DATA.md

Available test datasets

Datasets available in the SCIL DVC data repository.

Entries are indexed by archive name.

commit_amico.zip

• dwi.bvec
• peaks.nii.gz
• dwi.nii.gz
• md.nii.gz
• dwi.bval
• ad.nii.gz
• mask.nii.gz
• tracking.trk
• cmd
• wm_frf.txt
• fa.nii.gz
• gm_frf.txt
• csf_frf.txt

bundles.zip

• sagittal_3d.png
• sagittal_glass.png
• axial_glass.png
• coronal_3d.png
• axial_3d.png
• bundle_all_1mm.trk
• clusters.pkl
• bundle_0_binary.json
• coronal_glass.png
• bundle_0_measures.json
• bundle_all_1mm_ic.trk
• transformation_rigid.txt
• bundle_0_similarity.json
• bash.sh
• affine.txt
• config.json
• bundle_0_reco.tck
• bundle_all_1mm.nii.gz
• default_config_sim.json
• .gitignore
• bundle_all_1mm.nii.gz
• bundle_0.trk
• bundle_4.trk
• bundle_3.trk
• bundle_6.trk
• bundle_5.trk
• bundle_2.trk
• bundle_1.trk
• .gitignore
• bundle_0.trk
• bundle_4.trk
• bundle_3.trk
• bundle_6.trk
• bundle_5.trk
• bundle_2.trk
• bundle_1.trk
• .gitignore
• bundle_0.trk
• bundle_4.trk
• bundle_3.trk
• bundle_6.trk
• bundle_5.trk
• bundle_2.trk
• bundle_1.trk
• .gitignore
• bundle_0.trk
• bundle_4.trk
• bundle_3.trk
• bundle_6.trk
• bundle_5.trk
• bundle_2.trk
• results.json
• bundle_1.trk
• logfile.txt
• .gitignore

stats.zip

• participants.tsv
• meanstd_all.json
• .gitignore
• sub-1230_afd_total.npy
• sub-2120_fa.npy
• sub-2120_ad.npy
• sub-1108_md.npy
• sub-1230_ad.npy
• sub-1005_fa.npy
• sub-1005_nufo.npy
• sub-1108_ad.npy
• sub-2120_afd_fixel.npy
• sub-1230_nufo.npy
• sub-2120_nufo.npy
• sub-2120_md.npy
• sub-1005_md.npy
• sub-1005_ad.npy
• sub-1230_afd_fixel.npy
• list_id.txt
• sub-1005_afd_fixel.npy
• sub-1108_fa.npy
• sub-1005_rd.npy
• sub-1108_afd_fixel.npy
• sub-1230_rd.npy
• sub-1230_fa.npy
• sub-1230_md.npy
• sub-1108_afd_total.npy
• sub-2120_rd.npy
• sub-1005_afd_total.npy
• .gitignore
• sub-1108_rd.npy
• sub-2120_afd_total.npy
• sub-1108_nufo.npy

bst.zip

• todi_mask.nii.gz
• template_lin.nii.gz
• output0GenericAffine.mat
• rpt_m_lin.trk
• lw_todi_sh.nii.gz
• fodf.nii.gz
• out_lw_tdi.nii.gz
• bash.sh
• output1InverseWarp.nii.gz
• rpt_m_warp.trk
• mask.nii.gz
• fa.nii.gz
• todi_mask.nii.gz
• priors.nii.gz
• endpoints_mask.nii.gz
• .gitignore
• efod.nii.gz
• rpt_m.trk
• template0.nii.gz
• .gitignore

filtering.zip

• centroids.trk
• bundle_4_filtered.nii.gz
• bundle_all_1mm.trk
• sc.bdo
• bundle_all_1mm_inliers.trk
• bundle_4.trk
• mosaic.png
• voting_voxels.nii.gz
• voting_streamlines.trk
• bash.sh
• mask.nii.gz
• bundle_4_filtered_no_loops.trk
• bundle_all_1mm.nii.gz
• bundle_4_filtered.trk
• cluster_2.trk
• cluster_0.trk
• cluster_12.trk
• cluster_10.trk
• cluster_4.trk
• cluster_13.trk
• cluster_18.trk
• cluster_3.trk
• cluster_6.trk
• cluster_9.trk
• cluster_8.trk
• cluster_11.trk
• cluster_19.trk
• cluster_1.trk
• cluster_16.trk
• cluster_17.trk
• cluster_15.trk
• cluster_5.trk
• cluster_7.trk
• .gitignore
• cluster_14.trk

ihMT.zip

• echo-3_acq-altnp_ihmt.nii.gz
• echo-1_acq-pos_ihmt.json
• echo-2_acq-pos_ihmt.json
• echo-3_acq-neg_ihmt.nii.gz
• mask_resample.nii.gz
• echo-1_acq-mtoff_ihmt.json
• echo-1_acq-altpn_ihmt.json
• echo-3_acq-altpn_ihmt.nii.gz
• echo-1_acq-altpn_ihmt.nii.gz
• echo-1_acq-T1w_ihmt.nii.gz
• echo-3_acq-altpn_ihmt.json
• echo-2_acq-pos_ihmt.nii.gz
• echo-3_acq-T1w_ihmt.json
• echo-3_acq-altnp_ihmt.json
• echo-3_acq-mtoff_ihmt.nii.gz
• echo-1_acq-pos_ihmt.nii.gz
• echo-3_acq-neg_ihmt.json
• echo-2_acq-neg_ihmt.json
• echo-3_acq-T1w_ihmt.nii.gz
• echo-2_acq-neg_ihmt.nii.gz
• echo-2_acq-mtoff_ihmt.json
• echo-2_acq-altnp_ihmt.nii.gz
• echo-2_acq-altpn_ihmt.nii.gz
• echo-2_acq-altnp_ihmt.json
• echo-3_acq-pos_ihmt.json
• echo-2_acq-T1w_ihmt.json
• echo-3_acq-pos_ihmt.nii.gz
• echo-2_acq-mtoff_ihmt.nii.gz
• B1map.nii.gz
• B1map.json
• echo-2_acq-altpn_ihmt.json
• echo-1_acq-altnp_ihmt.nii.gz
• echo-1_acq-neg_ihmt.nii.gz
• echo-2_acq-T1w_ihmt.nii.gz
• echo-1_acq-neg_ihmt.json
• echo-1_acq-altnp_ihmt.json
• echo-1_acq-mtoff_ihmt.nii.gz
• echo-1_acq-T1w_ihmt.json
• echo-3_acq-mtoff_ihmt.json

tractometry.zip

• IFGWM.nii.gz
• label.npz
• tail.nii.gz
• IFGWM_uni_c_10.trk
• length_stats_1.json
• IFGWM_color.trk
• metric_label.json
• length_stats_2.json
• mni_masked.nii.gz
• IFGWM.trk
• IFGWM_uni_c.trk
• IFGWM_uni.trk
• length_stats.xlsx
• bash.sh
• distance.npz
• IFGWM_labels_map.nii.gz
• head.nii.gz
• IFGWM_mni_masked.png
• .gitignore

bids_json.zip

• result_complex_dwi_epi.json
• result_real_dwi_real_rev_dwi_sbref.json
• result_real_dwi_real_rev_dwi.json
• result_complex_dwi_complex_rev_dwi_sbref.json
• result_real_dwi_real_sbref.json
• result_complex_dwi_complex_sbref.json
• result_complex_dwi_complex_rev_dwi.json
• result_real_dwi_epi.json

MT.zip

• sub-001_echo-3_acq-mton_mtsat.json
• sub-001_echo-1_acq-t1w_mtsat.json
• sub-001_echo-1_acq-mtoff_mtsat.nii.gz
• sub-001_echo-4_acq-mtoff_mtsat.json
• sub-001_run-01_B1map.json
• sub-001_echo-4_acq-t1w_mtsat.json
• sub-001_echo-1_acq-mton_mtsat.json
• sub-001_echo-3_acq-mtoff_mtsat.json
• sub-001_echo-3_acq-mton_mtsat.nii.gz
• sub-001_echo-4_acq-mton_mtsat.json
• sub-001_echo-5_acq-mtoff_mtsat.json
• sub-001_echo-4_acq-t1w_mtsat.nii.gz
• sub-001_echo-1_acq-mton_mtsat.nii.gz
• sub-001_echo-2_acq-mtoff_mtsat.json
• sub-001_echo-1_acq-t1w_mtsat.nii.gz
• sub-001_echo-5_acq-mton_mtsat.json
• sub-001_echo-5_acq-t1w_mtsat.json
• sub-001_run-01_B1map.nii.gz
• sub-001_echo-2_acq-t1w_mtsat.nii.gz
• sub-001_echo-4_acq-mtoff_mtsat.nii.gz
• sub-001_echo-5_acq-mton_mtsat.nii.gz
• sub-001_echo-3_acq-t1w_mtsat.json
• sub-001_echo-2_acq-mton_mtsat.nii.gz
• sub-001_echo-5_acq-t1w_mtsat.nii.gz
• sub-001_echo-2_acq-mtoff_mtsat.nii.gz
• sub-001_echo-2_acq-t1w_mtsat.json
• sub-001_echo-3_acq-t1w_mtsat.nii.gz
• mask.nii.gz
• sub-001_echo-1_acq-mtoff_mtsat.json
• sub-001_echo-3_acq-mtoff_mtsat.nii.gz
• sub-001_echo-4_acq-mton_mtsat.nii.gz
• sub-001_echo-2_acq-mton_mtsat.json
• sub-001_echo-5_acq-mtoff_mtsat.nii.gz

btensor_testdata.zip

• planar.bvals
• dwi_spherical.nii.gz
• dwi_planar.nii.gz
• md.nii.gz
• dwi_linear.nii.gz
• linear.bvals
• linear.bvecs
• planar.bvecs
• spherical.bvecs
• wm_frf.txt
• fa.nii.gz
• gm_frf.txt
• csf_frf.txt
• spherical.bvals

tracking.zip

• seeding_mask.nii.gz
• interface.nii.gz
• map_exclude_corr.nii.gz
• peaks.nii.gz
• map_gm.nii.gz
• map_wm.nii.gz
• pft.trk
• union.trk
• fodf.nii.gz
• union_shuffle.trk
• map_csf.nii.gz
• local_split_2.trk
• map_include_corr.nii.gz
• bash.sh
• local_split_0.trk
• local_split_1.trk
• local.trk
• fa.nii.gz
• union_shuffle_sub.trk
• map_include.nii.gz
• map_exclude.nii.gz
• union_shuffle_sub_smooth.trk

atlas.zip

• brainstem_bin.nii.gz
• brainstem.nii.gz
• brainstem_174.nii.gz
• atlas_freesurfer_v2_labels_list.txt
• brainstem_173.nii.gz
• atlas_freesurfer_v2_single_brainstem_dil.nii.gz
• atlas_freesurfer_v2_LUT.json
• bash.sh
• atlas_freesurfer_v2_single_brainstem.nii.gz
• atlas_freesurfer_v2_no_brainstem.nii.gz
• brainstem_175.nii.gz
• atlas_freesurfer_v2.nii.gz
• 1031.nii.gz
• 2001.nii.gz
• 18.nii.gz
• 2023.nii.gz
• 60.nii.gz
• 1000.nii.gz
• 2000.nii.gz
• 1016.nii.gz
• 1018.nii.gz
• 2014.nii.gz
• 1021.nii.gz
• 1033.nii.gz
• 1032.nii.gz
• 1002.nii.gz
• 2034.nii.gz
• 2021.nii.gz
• 2028.nii.gz
• 10.nii.gz
• 1017.nii.gz
• 2012.nii.gz
• 2013.nii.gz
• 2005.nii.gz
• 28.nii.gz
• 1027.nii.gz
• 2011.nii.gz
• 1026.nii.gz
• 173.nii.gz
• 2008.nii.gz
• 1034.nii.gz
• 47.nii.gz
• 2017.nii.gz
• 53.nii.gz
• 1009.nii.gz
• 1005.nii.gz
• 1020.nii.gz
• 58.nii.gz
• 1025.nii.gz
• 17.nii.gz
• 175.nii.gz
• 2024.nii.gz
• 2022.nii.gz
• 51.nii.gz
• 1013.nii.gz
• 1019.nii.gz
• 1011.nii.gz
• 11.nii.gz
• 26.nii.gz
• 2019.nii.gz
• 1010.nii.gz
• 85.nii.gz
• 1003.nii.gz
• 2009.nii.gz
• 2031.nii.gz
• 50.nii.gz
• 2007.nii.gz
• 1024.nii.gz
• 2035.nii.gz
• 1022.nii.gz
• 2030.nii.gz
• 1030.nii.gz
• 2016.nii.gz
• 1008.nii.gz
• 2015.nii.gz
• 8_10.nii.gz
• 2033.nii.gz
• 2027.nii.gz
• 1006.nii.gz
• 1015.nii.gz
• 2018.nii.gz
• 2010.nii.gz
• 1001.nii.gz
• 1023.nii.gz
• 1035.nii.gz
• 2029.nii.gz
• 2032.nii.gz
• 1029.nii.gz
• 2025.nii.gz
• 2006.nii.gz
• 13.nii.gz
• 1028.nii.gz
• 52.nii.gz
• 2002.nii.gz
• .gitignore
• 1014.nii.gz
• 54.nii.gz
• 2003.nii.gz
• 1012.nii.gz
• 8.nii.gz
• 2020.nii.gz
• 174.nii.gz
• 2026.nii.gz
• 12.nii.gz
• 49.nii.gz
• right_fusiform.nii.gz
• left_ventraldc.nii.gz
• right_thalamus_proper.nii.gz
• left_rostral_middle_frontal.nii.gz
• left_parahipocampal.nii.gz
• right_pericalcarine.nii.gz
• right_parahipocampal.nii.gz
• left_superior_parietal.nii.gz
• left_parsopercularis.nii.gz
• left_frontal_pole.nii.gz
• right_posteriorcingulate.nii.gz
• left_lingual.nii.gz
• right_ventraldc.nii.gz
• right_isthmus_cingulate.nii.gz
• right_parstriangularis.nii.gz
• left_paracentral.nii.gz
• right_parsorbitalis.nii.gz
• right_banks_superior_temporal.nii.gz
• left_pallidum.nii.gz
• right_accumbens_area.nii.gz
• left_postcentral.nii.gz
• left_amygdala.nii.gz
• right_cuneus.nii.gz
• right_corpus_callosum.nii.gz
• right_frontal_pole.nii.gz
• right_lingual.nii.gz
• right_hippocampus.nii.gz
• left_hippocampus.nii.gz
• right_postcentral.nii.gz
• right_transverse_temporal.nii.gz
• right_medial_orbitofrontal.nii.gz
• left_precuneus.nii.gz
• right_inferior_temporal.nii.gz
• left_inferior_temporal.nii.gz
• right_precentral.nii.gz
• right_superior_parietal.nii.gz
• right_superior_frontral.nii.gz
• left_lateral_occipital.nii.gz
• pons.nii.gz
• left_precentral.nii.gz
• right_rostral_anterior_cingulate.nii.gz
• left_banks_superior_temporal.nii.gz
• left_inferior_parietal.nii.gz
• oblongata.nii.gz
• left_thalamus_proper.nii.gz
• left_fusiform.nii.gz
• left_putamen.nii.gz
• right_rostral_middle_frontal.nii.gz
• right_entorhinal.nii.gz
• left_temporal_pole.nii.gz
• left_supra_marginal.nii.gz
• left_laterral_orbitofrontal.nii.gz
• left_insula.nii.gz
• right_laterral_orbitofrontal.nii.gz
• right_supra_marginal.nii.gz
• left_isthmus_cingulate.nii.gz
• right_caudal_anterior_cingulate.nii.gz
• left_superior_frontral.nii.gz
• left_corpus_callosum.nii.gz
• left_posteriorcingulate.nii.gz
• right_amygdala.nii.gz
• left_pericalcarine.nii.gz
• right_caudal_middle_fontral.nii.gz
• right_inferior_parietal.nii.gz
• right_temporal_pole.nii.gz
• right_caudate.nii.gz
• right_middle_temporal.nii.gz
• right_lateral_occipital.nii.gz
• left_caudal_anterior_cingulate.nii.gz
• left_transverse_temporal.nii.gz
• left_rostral_anterior_cingulate.nii.gz
• left_middle_temporal.nii.gz
• left_cerebellum_cortex.nii.gz
• right_parsopercularis.nii.gz
• left_parsorbitalis.nii.gz
• left_medial_orbitofrontal.nii.gz
• right_insula.nii.gz
• right_precuneus.nii.gz
• left_entorhinal.nii.gz
• left_parstriangularis.nii.gz
• left_cuneus.nii.gz
• left_accumbens_area.nii.gz
• left_caudal_middle_fontral.nii.gz
• right_superior_temporal.nii.gz
• left_caudate.nii.gz
• .gitignore
• left_superior_temporal.nii.gz
• right_cerebellum_cortex.nii.gz
• right_putamen.nii.gz
• right_pallidum.nii.gz
• right_paracentral.nii.gz
• midbrain.nii.gz

anatomical_filtering.zip

• wmparc_filter_ana.nii.gz
• tractogram_filter_ana.trk

connectivity.zip

• labels_list.txt
• sc_add_10.npy
• sc.npy
• sc_reo_fake.npy
• len.npy
• bundle_all_1mm.trk
• sc_thr.npy
• endpoints_atlas.nii.gz
• sc_masked.npy
• decompose_afd_rd.h5
• fodf.nii.gz
• mask.npy
• vol.npy
• success.txt
• sc_norm.png
• sim.npy
• sc_lower_threshold.npy
• afd_max.npy
• bash.sh
• pval.npy
• gtm.json
• sc_normalize.npy
• affine.txt
• sc_norm_vol.npy
• reorder.txt
• decompose.h5
• afd_max.nii.gz
• sc_norm.npy
• 2_7.nii.gz
• 1_7.nii.gz
• 3_7.nii.gz
• 5_6.nii.gz
• 4_8.nii.gz
• 1_10.nii.gz
• 9_9.nii.gz
• .gitignore
• 4_8.trk
• 9_9.trk
• 1_10.trk
• 5_6.trk
• 1_7.trk
• 2_7.trk
• 3_7.trk
• .gitignore

plot.zip

• mask_wm.nii.gz
• atlas_brainnetome.nii.gz
• mask_gm.nii.gz
• map_gm.nii.gz
• map_wm.nii.gz
• ad.nii.gz
• atlas_brainnetome.json
• fa.nii.gz

others.zip

• t1_crop_denoised.nii.gz
• fibercup_bundle_0_color.trk
• encoding.b
• rgb_.nii.gz
• density.nii.gz
• IFGWM.trk
• IFGWM_sub.trk
• empty.trk
• fibercup_bundle_0.trk
• t1_resample.nii.gz
• t1_reshape.nii.gz
• t1_crop.nii.gz
• atlas_freesurfer_v2_LUT.json
• bash.sh
• rgb.nii.gz
• fa_resample.nii.gz
• t1.nii.gz
• fibercup_bundles.trk
• fibercup_bundles_color.trk
• fa.nii.gz
• atlas_freesurfer_v2.nii.gz

fodf_filtering.zip

• fodf_descoteaux07_sub_twice.nii.gz
• fodf_descoteaux07_sub.nii.gz
• fodf_descoteaux07_sub_full.nii.gz
• fodf_descoteaux07_sub_sym.nii.gz

processing.zip

• dki_fa.nii.gz
• ad_ransanc.nii.gz
• 1000_flip.b
• dki_ad.nii.gz
• dwi.bvec
• dwi_crop_1000.nii.gz
• nufo.nii.gz
• peaks.nii.gz
• frf.txt
• rd.nii.gz
• mni_masked_2x2x2.nii.gz
• afd_tot.nii.gz
• afd_test.nii.gz
• dwi_crop_n4.nii.gz
• sh_3000.nii.gz
• dwi_crop.nii.gz
• fodf_bingham.nii.gz
• bias_field_b0.nii.gz
• fa_low.nii.gz
• afd_sum.nii.gz
• 1000.b
• dwi.nii.gz
• fodf.nii.gz
• dwi_SNR.json
• 1000.bvec
• fodf_descoteaux07_sub.nii.gz
• fodf_descoteaux07.nii.gz
• small_roi_gm_mask.nii.gz
• sh_1000.nii.gz
• diff.nii.gz
• b0_mean.nii.gz
• 3000.bval
• 3000.bvec
• md.nii.gz
• fa_thr.nii.gz
• sh.nii.gz
• dwi.bval
• 1000.bval
• rd_test.nii.gz
• seed.nii.gz
• dki_md.nii.gz
• ad.nii.gz
• fodf_descoteaux07_sub_full.nii.gz
• cc.nii.gz
• nfrf.txt
• mfrf.txt
• fd.nii.gz
• dwi_graph.png
• dwi_crop_3000.nii.gz
• b0_mean_n4.nii.gz
• afd_max.nii.gz
• tracking.trk
• dwi_noise_mask.nii.gz
• fa.nii.gz
• dki_rd.nii.gz
• coronal.png
• axial.png
• sagittal.png
• .gitignore

surface_vtk_fib.zip

• gyri_fanning_c.trk
• gyri_fanning.fib
• rhpialt.vtk
• lh.pialt_xform
• gyri_fanning.trk
• lhpialt_lin.vtk
• fa_flip.nii.gz
• bash.sh
• lhpialt.vtk
• lhpialt_smooth.vtk
• affine.txt
• gyri_fanning.tck
• log.txt
• fa.nii.gz

tractograms.zip

• bundle_4_endpoints_5points.nii.gz
• bundle_4_endpoints_1point.nii.gz
• bundle_4.tck
• bundle_4_center.nii.gz
• bundle_4_head_tail_offset.nii.gz
• bundle_4_wm.nii.gz
• bundle_4_cut_center.tck
• bundle_4_head_tail.nii.gz
• bundle_4_cut_endpoints.tck
• .gitignore
• bundle_4_endpoints_5points.nii.gz
• bundle_4_endpoints_1point.nii.gz
• bundle_4.tck
• bundle_4_center.nii.gz
• bundle_4_head_tail_offset.nii.gz
• bundle_4_wm.nii.gz
• bundle_4_cut_center.tck
• bundle_4_head_tail.nii.gz
• bundle_4_cut_endpoints.tck
• .gitignore

registration.zip

• mni_masked_2x2x2.nii.gz
• output0GenericAffine.mat
• b0.nii.gz
• output1Warp.nii.gz
• output1InverseWarp.nii.gz

topup_eddy.zip

• topup_results_movpar.txt
• sub-01_dir-AP_sbref.nii.gz
• topup_results_fieldcoef.nii.gz
• sub-01__corrected_b0s.nii.gz
• sub-01_dir-AP_dwi.bvec
• sub-01_dir-PA_dwi.bval
• sub-01_dir-PA_sbref.nii.gz
• sub-01_dir-PA_dwi.nii.gz
• sub-01_dir-PA_dwi.bvec
• sub-01_dir-AP_dwi.nii.gz
• sub-01_dir-AP_dwi.bval

topup_eddy_light.zip

• topup_results_movpar.txt
• sub-01_dir-AP_sbref.nii.gz
• topup_results_fieldcoef.nii.gz
• sub-01__corrected_b0s.nii.gz
• sub-01_dir-AP_dwi.bvec
• sub-01_dir-PA_dwi.bval
• sub-01_dir-PA_sbref.nii.gz
• sub-01_dir-PA_dwi.nii.gz
• sub-01_dir-PA_dwi.bvec
• sub-01_dir-AP_dwi.nii.gz
• sub-01_dir-AP_dwi.bval

bids.zip

• .bidsignore
• dataset_description.json
• sub-01_ses-001_T1w.json
• sub-01_ses-001_dir-AP_dwi.json
• sub-01_ses-001_dir-PA_epi.json
• sub-01_ses-001_dir-AP_epi.json

antsbet.zip

• t1_template.nii.gz
• t1_unaligned.nii.gz
• t1_brain_probability_map.nii.gz
• t1_unaligned_brainmask.nii.gz
• t1.nii.gz

freesurfer.zip

• license.txt
• anat_image.nii.gz
• t1.nii.gz
• fa.nii.gz

light.zip

• s1__iso_diff.txt
• s2__para_diff.txt
• s1__para_diff.txt
• s2__iso_diff.txt
• box_3d_mask.nii.gz
• box_3d_image.nii.gz

heavy.zip

• wmparc.nii.gz
• aparc_aseg.nii.gz
• dwi.nii.gz
• b0.nii.gz
• mask.nii.gz
• anat_mask.nii.gz
• anat_image.nii.gz
• dwi.bvec
• dwi.nii.gz
• dwi.bval
• mask.nii.gz
• t1_template.nii.gz
• t1_brain_probability_map.nii.gz