dwi2cond

Description

This optional tool prepares diffusion tensors for GM and WM from diffusion MRI (dMRI) data. The prepared tensors can then be used by SimNIBS to estimate anisotropic conductivities for GM and WM during the FEM calculations. Only single shell data (i.e., with a single b-value in addition to some b=0 images) with a single phase encoding direction for the EPI readout is supported. All processing steps are based on FSL tools.

Attention

dwi2cond depends on FSL (5.0.5 or newer), and is therefore not compatible with Windows. Please see Optional Dependencies for instructions on how to set-up FSL

Usage example

  1. Open a terminal and go to the directory of the “Ernie” example data set.

  2. Run:

dwi2cond --all --eddy --phasedir=-y --readout=0.05 ernie org/ernie_dMRI.nii.gz org/ernie_dMRI.bval org/ernie_dMRI.bvec org/ernie_dMRI_rev.nii.gz

The argument --all tells dwi2cond to preprocess the diffusion MRI data, reconstruct the diffusion tensors, and register the tensors to the T1 of the subject. Preprocessing encompasses correction for subject motion and eddy-current-induced image distortions and, optionally, correction for static image distortions.

Setting --eddy will prompt dwi2cond to use FSL eddy for motion and eddy-current correction. In this case, also the phase encoding direction of the dMRI sequence and its readout time (in [s]) has to be stated using --phasedir and --readout. Please refer to the description of FSL eddy on the FSL homepage for further information about these parameters.

The subject ID is provided as first parameter after the arguments, followed by the name of the diffusion dataset and the text files for the b-values and the b-vectors. Please refer to the description of FSL dtifit for details on the file conventions.

A dataset of b=0 images acquired with reversed phase encoding direction is given as last parameter. In this case, FSL topup will be used for static distortion correction.

  1. Check the results:

dwi2cond –check ernie

This shows the fractional anisotropy (FA) image superimposed on the structural T1 of the subject in fslview or fsleyes for visual control of the coregistration accuracy. In a second viewer, FA images determined from the dMRI data before and after preprocessing are shown to allow for controlling the effects of the preprocessing. These FA images are registered to the T1 using a rigid body (6DoF) transformation, so that spatial distortions remain visible. Finally, also sum-of-squared-error (SSE) images of the tensor fitting procedure are shown. The SSE images are in arbitrary units, but are helpful to check the effectiveness of the preprocessing steps and to identify putative artifacts in the dMRI data. Finally, the first eigenvectors of the tensors are shown in gmsh for checking their orientation.

Further notes

  • Dwi2cond uses a non-linear registration based on FSL fnirt to transform the diffusion tensors to the space of the structural T1 image. In case the distortion correction during preprocessing is good enough, 12 or 6 DoF affine registrations can be used instead (controlled by the argument –regmthd).

  • dwi2cond also supports distortion correction based on fieldmaps: dwi2cond --all --dwidwell=<dwell_time_in_ms> --udir=<warping_direction> <subjectID> <dMRI_dataset> <bvalue_file> <bvector_file> <field_map_magnitude_image> <field_map_phase_image>

  • The argument --dwidwell is used to specify the dwell-time (or echo-spacing) of the dMRI sequence in [ms]. The standard warping direction is set to “y-”, otherwise state it using --udir. A standard Siemens gre fieldmap with a TE difference of 2.46 ms is assumed. For other fieldmaps, additional parameters have to be defined on the command line (see dwi2cond –help).

  • Alternatively, you can use your own preprocessed DTI data as input

dwi2cond --all <subjectID> <DTI-tensor>

Dwi2cond will coregister the tensor image with the structural T1 of the subject for further use with SimNIBS.

  • When something goes wrong, you can check the dwi2cond_log.html which is saved in the d2c_subID subdirectory.

  • SimNIBS will use the coregistered diffusion tensors (stored in d2c_subID/dti_results_T1space/DTI_conf_tensor.nii.gz) to estimate conductivity tensors for GM and WM. The following mappings from diffusion to conductivity tensors are supported:

  • Direct mapping based on linear rescaling of the diffusion tensors (Rullmann et al., 2009; Tuch et al., 2001).

  • Inhomogeneous, isotropic conductivities, calculated as the mean conductivities of tensors of the direct mapping approach.

  • Volume normalized mapping (Güllmar et al., 2010) that keeps the geometric mean of the eigenvalues identical to the standard isotropic conductivity.

  • SimNIBS ensures that all conductivity tensors are positive definite. This is done to ensure that the FEM solver will robustly converge. In addition, a maximal conductivity of 2 S/m and a maximal ratio of 10 between the largest and smallest conductivity eigenvalues is enforced to guarantee a realistic conductivity range. The latter values can be changed in the GUI or scripts.