Title: High quality white matter reference tracts

Type Dataset Wasserthal Jakob, Neher Peter, Maier-Hein Klaus (2018): High quality white matter reference tracts. Zenodo. Dataset. https://zenodo.org/record/1201476

Authors: Wasserthal Jakob (Division of Medical Image Computing, German Cancer Research Center) ; Neher Peter (Division of Medical Image Computing, German Cancer Research Center) ; Maier-Hein Klaus (Division of Medical Image Computing, German Cancer Research Center) ;

Links

• Item record in Zenodo
• Digital object URL

Summary

This dataset contains segmentations of 72 white matter tracts obtained from 10 subjects included in the Human Connectome Project (HCP) young adult dataset (https://www.humanconnectome.org/study/hcp-young-adult). The folder names correspond to the ID of the HCP subjects.

The data is part of the following project: https://github.com/MIC-DKFZ/TractSeg/ If you use the data please cite the paper mentioned on the project page.

The tracts were extracted semi-automatically from whole-brain tractograms. For a detailed description of the tract segmentation process please refer to the paper linked on the project page. The following MRtrix (http://www.mrtrix.org/) commands were used to obtain the whole-brain tractograms:

5ttgen fsl T1w_acpc_dc_restore_brain.nii.gz 5TT.mif -premasked dwi2response msmt_5tt Diffusion.nii.gz 5TT.mif RF_WM.txt RF_GM.txt RF_CSF.txt -voxels RF_voxels.mif -fslgrad Diffusion.bvecs Diffusion.bvals dwi2fod msmt_csd Diffusion.nii.gz RF_WM.txt WM_FODs.mif RF_GM.txt GM.mif RF_CSF.txt CSF.mif -mask nodif_brain_mask.nii.gz -fslgrad Diffusion.bvecs Diffusion.bvals tckgen -algorithm iFOD2 WM_FODs.mif output.tck -act 5TT.mif -backtrack -crop_at_gmwmi -seed_image nodif_brain_mask.nii.gz -maxlength 250 -minlength 40 -number 10M -cutoff 0.06 -maxnum 0

For "CA", "IFO_left", "IFO_right", "UF_left", "UF_right" we used tracking without anatomical constraints:

tckgen -algorithm iFOD2 WM_FODs.mif output.tck -seed_image nodif_brain_mask.nii.gz -maxlength 250 -minlength 40 -number 10M -cutoff 0.06 -maxnum 0

Due to their enormous size, the whole brain tractograms corresponding to the segmented tracts are not included this dataset. Please contact the author of the paper if you are interested in these tractograms.

The following white matter tracts are included:

1: AF_left         (Arcuate fascicle) 2: AF_right 3: ATR_left        (Anterior Thalamic Radiation) 4: ATR_right 5: CA              (Commissure Anterior) 6: CC_1            (Rostrum) 7: CC_2            (Genu) 8: CC_3            (Rostral body (Premotor)) 9: CC_4            (Anterior midbody (Primary Motor)) 10: CC_5           (Posterior midbody (Primary Somatosensory)) 11: CC_6           (Isthmus) 12: CC_7           (Splenium) 13: CG_left        (Cingulum left) 14: CG_right    15: CST_left       (Corticospinal tract 16: CST_right  17: MLF_left       (Middle longitudinal fascicle) 18: MLF_right 19: FPT_left       (Fronto-pontine tract) 20: FPT_right  21: FX_left        (Fornix) 22: FX_right 23: ICP_left       (Inferior cerebellar peduncle) 24: ICP_right  25: IFO_left       (Inferior occipito-frontal fascicle)  26: IFO_right 27: ILF_left       (Inferior longitudinal fascicle)  28: ILF_right  29: MCP            (Middle cerebellar peduncle) 30: OR_left        (Optic radiation)  31: OR_right 32: POPT_left      (Parieto‐occipital pontine) 33: POPT_right  34: SCP_left       (Superior cerebellar peduncle) 35: SCP_right  36: SLF_I_left     (Superior longitudinal fascicle I) 37: SLF_I_right  38: SLF_II_left    (Superior longitudinal fascicle II) 39: SLF_II_right 40: SLF_III_left   (Superior longitudinal fascicle III) 41: SLF_III_right  42: STR_left       (Superior Thalamic Radiation) 43: STR_right  44: UF_left        (Uncinate fascicle)  45: UF_right  46: CC             (Corpus Callosum - all) 47: T_PREF_left    (Thalamo-prefrontal) 48: T_PREF_right  49: T_PREM_left    (Thalamo-premotor) 50: T_PREM_right  51: T_PREC_left    (Thalamo-precentral) 52: T_PREC_right  53: T_POSTC_left   (Thalamo-postcentral) 54: T_POSTC_right  55: T_PAR_left     (Thalamo-parietal) 56: T_PAR_right  57: T_OCC_left     (Thalamo-occipital) 58: T_OCC_right  59: ST_FO_left     (Striato-fronto-orbital) 60: ST_FO_right  61: ST_PREF_left   (Striato-prefrontal) 62: ST_PREF_right  63: ST_PREM_left   (Striato-premotor) 64: ST_PREM_right  65: ST_PREC_left   (Striato-precentral) 66: ST_PREC_right  67: ST_POSTC_left  (Striato-postcentral) 68: ST_POSTC_right 69: ST_PAR_left    (Striato-parietal) 70: ST_PAR_right  71: ST_OCC_left    (Striato-occipital) 72: ST_OCC_right  

More information

• DOI: 10.5281/zenodo.1201476

Subjects

• dMRI, Tractography, White Matter, Human Connectome Project, Diffusion MRI, Connectomics, Segmentation

Dates

• Publication date: 2018
• Issued: March 16, 2018

Notes

Rights

• https://creativecommons.org/licenses/by-nc/4.0/legalcode Creative Commons Attribution Non Commercial 4.0 International
• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

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