Computational protocol: Topography of connections between human prefrontal cortex and mediodorsal thalamus studied with diffusion tractography

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Protocol publication

[…] Animal procedures were conducted with approval of the local committee on research animal care. A post-mortem macaque (Macaca fascicularis) brain was obtained from a previous study. The animal in question had undergone a 1 hour intravascular middle cerebral artery occlusion experiment and had sustained no permanent lesion as detectable using in vivo DWI. Following this the brain was removed after euthanasia and immersed in a 10% formaldehyde solution at 4 °C for at least 4 weeks. Following fixation, it was placed in a solution of 2% phosphate-buffered saline (PBS) doped with 1 mMol/l Gd-DTPA (Magnevist, Berlex Imaging, Montville, NJ, USA) contrast agent. The brain was then mounted on an individually modelled mould and immersed in Fomblin LC/8 (Solvay Solexis Inc., Thorofare, NJ, USA) for susceptibility matching.High angular and high spatial resolution diffusion-weighted images were acquired using previously described methods (). Imaging was performed on a 4.7 T/33 cm bore Oxford magnet equipped with BGA 12 gradients interfaced to a Bruker Biospec Avance console (ParaVision 3.0.1; Bruker Biospin, Ettlingen, Germany), using a standard 72 mm inner diameter birdcage coil (Bruker). DWI was performed using a 3D segmented spin-echo EPI sequence (430 µm isotropic resolution, TE 33 ms, 8 shots, TE 33 ms, TR 350 ms, 120 isotropically distributed diffusion directions, bmax = 8000, delta 6.85 ms, Delta 10.8 ms, 27 h total scan time). [...] Diffusion tractography (methods detailed below) was carried out in the untransformed space native to macaque or human subjects. Macaque results were then stored in the same native space. In order to compare results across individual human subjects, the human results were stored in MNI152 standard space for further processing. To transfer individual images into standard space, individual human structural MRIs were skull-stripped using the FMRIB software library (FSL) Brain Extraction Tool (BET) () and registered to the skull-stripped registration target in MNI152 space using a multi-scale approach maximising correlation ratio () between image histograms () using the FSL linear image registration tool (FLIRT). The MNI152 registration target was defined at the Montréal Neurological Institute, averaging 152 stereotaxically normalized T1-weighted images of normal human brains. A copy is provided with the FSL software library () (http://www.fmrib.ox.ac.uk/fsl).For diffusion data, FLIRT was employed to establish registration parameters between a non diffusion-weighted reference volume and each individual anatomical MRI. The registration parameters that were derived were then concatenated with those transforming each individual structural MRI scan into standard space, resulting in transformation parameters taking individual DWIs into standard space. […]

Pipeline specifications

Software tools ParaVision, FSL, BET
Application Magnetic resonance imaging
Organisms Homo sapiens
Diseases Neural Tube Defects