workflows.dmri.fsl.utils

apply_all_corrections()

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Combines two lists of linear transforms with the deformation field map obtained typically after the SDC process. Additionally, computes the corresponding bspline coefficients and the map of determinants of the jacobian.

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cleanup_edge_pipeline()

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Perform some de-spiking filtering to clean up the edge of the fieldmap (copied from fsl_prepare_fieldmap)

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dwi_flirt()

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Generates a workflow for linear registration of dwi volumes

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vsm2warp()

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Converts a voxel shift map (vsm) to a displacements field (warp).

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add_empty_vol()

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Adds an empty vol to the phase difference image

b0_average()

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A function that averages the b0 volumes from a DWI dataset. As current dMRI data are being acquired with all b-values > 0.0, the lowb volumes are selected by specifying the parameter max_b.

Warning

b0 should be already registered (head motion artifact should be corrected).

b0_indices()

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Extract the indices of slices in a b-values file with a low b value

compute_readout()

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Computes readout time from epi params (see eddy documentation).

Warning

params['echospacing'] should be in sec units.

copy_hdr()

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demean_image()

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Demean image data inside mask

eddy_rotate_bvecs()

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Rotates the input bvec file accordingly with a list of parameters sourced from eddy, as explained here.

enhance()

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extract_bval()

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Writes an image containing only the volumes with b-value specified at input

hmc_split()

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Selects the reference and moving volumes from a dwi dataset for the purpose of HMC.

insert_mat()

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rads2radsec()

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Converts input phase difference map to rads

recompose_dwi()

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Recompose back the dMRI data accordingly the b-values table after EC correction

recompose_xfm()

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Insert identity transformation matrices in b0 volumes to build up a list

remove_comp()

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Removes the volume volid from the 4D nifti file

reorient_bvecs()

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Checks reorientations of in_dwi w.r.t. old_dwi and reorients the in_bvec table accordingly.

rotate_bvecs()

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Rotates the input bvec file accordingly with a list of matrices.

Note

the input affine matrix transforms points in the destination image to their corresponding coordinates in the original image. Therefore, this matrix should be inverted first, as we want to know the target position of \vec{r}.

siemens2rads()

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Converts input phase difference map to rads

time_avg()

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Average the input time-series, selecting the indices given in index

Warning

time steps should be already registered (corrected for head motion artifacts).