# Human Brain Database - Controls ## Description The datasets available in this folder regard the acquisition of high resolution MRI images of one cohort of adult subjects, on a 3 Tesla Philips scanner. The cohort is 15 normal subjects. The acquisition is carried out in the context of the work for Deliverable _D2.2 Human Brain Imaging Database_ (M18). Images are obtained at the USR _Center of Excellence for High Field Magnetic Resonance (CERMAC)_. **Scanner**: Philips Ingenia CX 3T Details: * 3 Tesla MR system * Software release 5.3 * 32 channel head coil ## Sequences (Raw\_Data) DICOM to NIfTI conversion is computed using dcm2niiX version v1.0.20190902 (https://www.nitrc.org/projects/mricrogl/). **3D\_FLAIR\_Tra** _Fluid-Attenuated Inversion Recovery volumetric acquisition for morphological characterization_ * Acquisition plane: Axial * TR/TE/TI (ms): 9000/290/2500 * Data matrix: 204 x 197 * Field of view (FOV) (mm): 230 x 222 * In-plane resolution (mm): 1.13 x 1.13 * Thickness (mm): 1.20 * Number of sections: 204 **B0\_reverse** _Sequence without diffusion-weighting for estimation and correction for susceptibility-induced distortions_ * Same geometrical parameters of the _raw\_data\_NODDI_ images * Acquired using a reversed phase-encoding direction (posterior-to-anterior) **raw\_data\_DTI\_32** _Diffusion Tensor Imaging acquisition_ * Acquisition plane: Axial * TR/TE (ms): 3850/92 * b-value (s/mm2): 0, 1000 * no. of gradient directions: 32 * SENSE factor: 2 * MultiBand factor: 2 * Data matrix: 128 x 128 * Field of view (FOV) (mm): 224 x 224 * In-plane resolution (mm): 1.75 x 1.75 * Thickness (mm): 2 * Number of sections: 60 **raw\_data\_NODDI** _Multi-compartmental dMRI sequence for advanced tractography and NODDI analyses_ * Axial high angular resolution diffusion-weighted imaging (HARDI) acquisition along 60 gradient directions at a b-value of 3000 s/mm2, * DTI acquisition along 35 directions at a b-value of 711 s/mm2 * 11 volumes without diffusion-weighting (b0 images) * The phase-encoding direction was anterior-to-posterior for all these acquisitions **s3DI\_MC\_HR** _Three-dimensional high-resolution time-of-flight (TOF) acquisition for arterial vessel visualization_ * Acquisition plane: Axial * TR/TE (ms): 23/3.5 Data matrix: 500 x 399 * Field of view (FOV) (mm): 200 x 200 * In-plane resolution (mm): 0.4 x 0.5 * Thickness (mm): 0.9 * Number of sections: 210 **SWIp\_axial** _Susceptibility-Weighted Imaging acquisition for venous vascular modeling_ * Acquisition plane: Axial * TR/TE (ms): 31/7.2 * Data matrix: 384 x 313 * Field of view (FOV) (mm): 230 x 189 * In-plane resolution (mm): 0.6 x 0.6 * Thickness (mm): 2.0 * Number of sections: 130 **T1\_3D\_PROSET\_Sag** _T1-weighted volumetric acquisition for morphological characterization_ * TR/TE (ms): 12/5.8 * Data matrix: 320 x 299 * Field of view (FOV) (mm): 256 x 240 * In-plane resolution (mm): 0.80 x 0.80 * Thickness (mm): 0.80 * Number of sections: 236 ## Maps ### DTI _Diffusion Tensor Imaging_ Tensorial diffusion maps at b-value = 1000 s/mm2. **AD\_map** _Axial Diffusivity Map_ **MD\_map** _Mean Diffusivity Map_ **RD\_map** _Radial Diffusivity Map_ **FA\_map** _Fractional Anisotropy Map_ **FAcolor\_map** _Color Coded Directional Fractional Anisotropy Map_ ### HARDI _High angular resolution diffusion-weighted imaging_ Same maps available in DTI at b-value = 3000 s/mm2. ### NODDI _Neurite orientation dispersion and density imaging_ Multi-compartment diffusion maps. The processing is based on this paper (https://www.ncbi.nlm.nih.gov/pubmed/22484410) and performed using a MATLAB toolbox available here (http://mig.cs.ucl.ac.uk/mig/mig/index.php/?n=Tutorial.NODDImatlab/) **ABS\_FECVF\_map** _Absolute Extra-cellular Volume Fraction_ **ABS\_FICVF\_map** _Absolute Intra-neurite Volume Fraction_ **FISO\_map** _Isotropic Fraction_ **ODI\_map** _Orientation Dispersion Index_ ### Tractography Tractography is computed using TrackVis (http://www.trackvis.org/). Two different types of files are available and in both cases XXX stands for the fibre bundle considered and YYY stands for the MRI sequence used for the alignment. **XXX\_on\_YYY.nii.gz** The fibres are overimposed _on_ the dataset and converted in NIfTI file format. **XXX\_to\_YYY.trk** The fibres are aligned _to_ the dataset but are represented as tracts alone in TrackVis file format. The definition of the TrackVis file format is available here (http://trackvis.org/docs/?subsect=fileformat).