#MIND PATH TO THALAMUS WALKTHROUGH TEXT REGISTRATION#
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This can be run after preprocessing or even before if the subject did not move too much: To check whether your bvecs and bvals are correct, it is recommended to run a quick check on the raw data. The order of entries in this file must match the order of volumes in the input data and entries in the gradient directions text file. The b values are assumed to be in s/mm^2 units. For volumes in which there was no diffusion weighting, the entry should still be present, although the direction of the vector does not matter! For technical details see this FAQ entry.ī values ( bvals): An ASCII text file containing a list of b values applied during each volume acquisition. Vectors are normalised to unit length within the dtifit code. The order of entries in this file must match the order of volumes in the input data series. Gradient directions ( bvecs): An ASCII text file containing a list of gradient directions applied during diffusion weighted volumes. This will include diffusion-weighted volumes and volume(s) with no diffusion weighting.

#MIND PATH TO THALAMUS WALKTHROUGH TEXT SERIES#

To run FDT tools we need:ĭiffusion weighted data ( ): A 4D series of data volumes. Generating a connectivity distribution from a single voxel of interest takes about 1 second)įurther post-processing of probtrackx outputs can be carried out if required using the command-line utilitiesĭiffusion data is usually stored in a 4D NIFTI file, where each volume is acquired with a different b-value and/or gradient orientation. Probtrackx - Probabilistic tractography run on the output of bedpostx (execution time depends very much on what the user wishes to do.

#MIND PATH TO THALAMUS WALKTHROUGH TEXT REGISTRATION#

Registration to structural reference image and/or standard space - (3-6 minutes).TBSS - Comparison of the fractional anisotropy maps (or others) between subjects (see TBSS)īedpostx - Fitting of the probabilistic diffusion model on corrected data (~15 hours single-threaded on CPU or less if multi-threaded or ~30 minutes run on GPU) For a microstructural analysis the further pipeline would be:ĭtifit - Fitting of diffusion tensors on eddy-corrected data (~1 minute) We can now either run a microstructural analysis or tractography. (~hours-days on CPU or less if multi-threaded or few hours on GPU).Īfter running eddy, all the diffusion-weighted images should be in alignment with each other and be undistorted. It can also use a fieldmap estimated by topup and correct for susceptibility-induced distortions. eddy simultaneously corrects for eddy currents and subject motion. Topup - Susceptibility-induced distortion correction (fieldmap estimation) using topup.īet - Brain extraction using BET on the distortion-corrected b0 (output of topup).Įddy - Distortion correction using eddy. To call the FDT GUI, either run Fdt ( Fdt_gui on a Mac), or run fsl and press the FDT button.Ī typical processing pipeline (and approximate time required for each stage, based on an Intel 2.66GHz processor, and a 60-direction whole-brain dataset of dimensions 128x128x70, at 2 mm isotropic resolution) would consist of:Īny study or scanner-specific pre-processing (e.g., conversion from DICOM to NIFTI using for example dcm2niix, removal of images affected by large artifacts). qboot - Estimation of fibre orientations using q-ball ODFs and residual bootstrap.PROBTRACKX - probabilistic tracking with crossing fibres.

Mind path to thalamus walkthrough text