aslprep.workflows.asl.hmc module

Workflows for estimating and correcting head motion in ASL images.

init_asl_hmc_wf(mem_gb, omp_nthreads, name='asl_hmc_wf')

Estimate head-motion parameters and optionally correct them for intensity differences.

This workflow separately estimates motion parameters for each unique type of volume (e.g., control, label, deltam, M0, CBF), and then stitches the resulting parameters back together according to the aslcontext file.

Workflow Graph

(Source code, png, svg, pdf)

Parameters:

• processing_target ({“control”, “deltam”, “cbf”})

• m0type ({“Separate”, “Included”, “Absent”, “Estimate”})

• mem_gb (float) – Size of ASL file in GB

• omp_nthreads (int) – Maximum number of threads an individual process may use

• name (str) – Name of workflow (default: asl_hmc_wf)

Inputs:

• asl_file – Control-label pair series NIfTI file. If an ASL run contains M0 volumes, deltaM volumes, or CBF volumes, those volumes should be removed before running this workflow.

• aslcontext – ASL context TSV file.

• raw_ref_image – Reference image to which ASL series is motion corrected

Outputs:

• xforms – ITKTransform file aligning each volume to ref_image

• movpar_file – MCFLIRT motion parameters, normalized to SPM format (X, Y, Z, Rx, Ry, Rz)

• rms_file – Framewise displacement as measured by fsl_motion_outliers

Notes

ASLPrep uses volume type-wise motion correction [1] instead of the zig-zag regression approach [2] because it is unclear how M0 volumes should be treated in the zig-zag method.

References

[1]

Ze Wang, Geoffrey K Aguirre, Hengyi Rao, Jiongjiong Wang, María A Fernández-Seara, Anna R Childress, and John A Detre. Empirical optimization of asl data analysis using an asl data processing toolbox: asltbx. Magnetic resonance imaging, 26(2):261–269, 2008. URL: https://doi.org/10.1016/j.mri.2007.07.003, doi:10.1016/j.mri.2007.07.003.

[2]

Ze Wang. Improving cerebral blood flow quantification for arterial spin labeled perfusion mri by removing residual motion artifacts and global signal fluctuations. Magnetic resonance imaging, 30(10):1409–1415, 2012. URL: https://doi.org/10.1016/j.mri.2012.05.004, doi:10.1016/j.mri.2012.05.004.

init_m0scan_hmc_wf(output_dir, mem_gb, omp_nthreads, name='m0scan_hmc_wf')

Estimate head-motion parameters for the M0 scan.

This workflow resamples the M0 scan to the ASL reference resolution/orientation, and then applies MCFLIRT to the M0 scan.

Workflow Graph

(Source code)

Parameters:

• output_dir (str) – Output directory for the M0 scan motion correction transforms

• mem_gb (float) – Memory usage for the workflow in GB.

• omp_nthreads (int) – Maximum number of threads an individual process may use

• name (str) – Name of workflow (default: m0scan_hmc_wf)

Inputs:

• m0scan – M0 scan NIfTI file.

• aslref – ASL reference image NIfTI file.

Outputs:

• m0scan2aslref_xfm – ITKTransform file aligning the M0 scan to the ASL reference.

• m0scan_aslref – Mean M0 scan image in ASL reference space. Used for fit report workflow.