AFQ.tasks.tissue

Attributes

logger

Functions

wm_gm_interface(pve_internal, data_imap)	full path to a nifti file containing the white
pve_internal(structural_imap[, pve])	WM+GM+CSF segmentation
msmt_params(structural_imap, data_imap, pve_internal, ...)	full path to a nifti file containing
msmt_apm(msmtcsd_params)	full path to a nifti file containing
msmt_aodf(msmtcsd_params, structural_imap, ...)	full path to a nifti file containing
msmt_aodf_asi(msmt_aodf_params, data_imap)	full path to a nifti file containing
msmt_aodf_opm(msmt_aodf_params, data_imap)	full path to a nifti file containing
msmt_aodf_nufid(msmt_aodf_params, data_imap, ...)	full path to a nifti file containing
csd_aodf_nufid(data_imap, pve_internal, tracking_params)	full path to a nifti file containing
get_tissue_plan(kwargs)

Module Contents

AFQ.tasks.tissue.logger

AFQ.tasks.tissue.wm_gm_interface(pve_internal, data_imap)

full path to a nifti file containing the white matter/gray matter interface

AFQ.tasks.tissue.pve_internal(structural_imap, pve='synthseg')

WM+GM+CSF segmentation

Parameters:

pvestr or PVEImage, optional

Method to use for PVE estimation. Can be a string defining a built-in method from neural networks, or a Definition object to import the PVE. Importing a PVE from software like Freesurfer or FSL FAST is recommended if they are available. The built-in methods are “synthseg” or “multiaxial+brainchop”. “synthseg” uses SynthSeg2 [1] to get the PVE. “multiaxial+brainchop” uses MultiAxial [2] and BrainChop [3] segmentations to get the PVE. Note this requires downloading the pre-trained multi-axial model which is licensed with Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International. Default: “synthseg”

AFQ.tasks.tissue.msmt_params(structural_imap, data_imap, pve_internal, citations, msmt_sh_order=8, msmt_fa_thr=0.7)

full path to a nifti file containing parameters for the MSMT CSD white matter fit, full path to a nifti file containing parameters for the MSMT CSD gray matter fit, full path to a nifti file containing parameters for the MSMT CSD cerebrospinal fluid fit

Parameters:

msmt_sh_orderint, optional.

Spherical harmonic order to use for the MSMT CSD fit. Default: 8

msmt_fa_thrfloat, optional.

The threshold on the FA used to calculate the multi shell auto response. Can be useful to reduce for baby subjects. Default: 0.7

References

[1]

B. Jeurissen, J.-D. Tournier, T. Dhollander, A. Connelly, and J. Sijbers. Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data. NeuroImage, 103 (2014), pp. 411–426

AFQ.tasks.tissue.msmt_apm(msmtcsd_params)

full path to a nifti file containing the anisotropic power map

AFQ.tasks.tissue.msmt_aodf(msmtcsd_params, structural_imap, tracking_params, citations)

full path to a nifti file containing MSMT CSD ODFs filtered by unified filtering [1]

References

[1] Poirier and Descoteaux, 2024, “A Unified Filtering Method for

Estimating Asymmetric Orientation Distribution Functions”, Neuroimage, https://doi.org/10.1016/j.neuroimage.2024.120516

AFQ.tasks.tissue.msmt_aodf_asi(msmt_aodf_params, data_imap)

full path to a nifti file containing the MSMT CSD Asymmetric Index (ASI) [1]

References

[1] S. Cetin Karayumak, E. Özarslan, and G. Unal,

“Asymmetric Orientation Distribution Functions (AODFs) revealing intravoxel geometry in diffusion MRI” Magnetic Resonance Imaging, vol. 49, pp. 145-158, Jun. 2018, doi: https://doi.org/10.1016/j.mri.2018.03.006.

AFQ.tasks.tissue.msmt_aodf_opm(msmt_aodf_params, data_imap)

full path to a nifti file containing the MSMT CSD odd-power map [1]

References

[1] C. Poirier, E. St-Onge, and M. Descoteaux,

“Investigating the Occurrence of Asymmetric Patterns in White Matter Fiber Orientation Distribution Functions” [Abstract], In: Proc. Intl. Soc. Mag. Reson. Med. 29 (2021), 2021 May 15-20, Vancouver, BC, Abstract number 0865.

AFQ.tasks.tissue.msmt_aodf_nufid(msmt_aodf_params, data_imap, tracking_params, pve_internal)

full path to a nifti file containing the MSMT CSD Number of fiber directions (nufid) map [1]

References

[1] C. Poirier and M. Descoteaux,

“Filtering Methods for Asymmetric ODFs: Where and How Asymmetry Occurs in the White Matter.” bioRxiv. 2022 Jan 1; 2022.12.18.520881. doi: https://doi.org/10.1101/2022.12.18.520881

AFQ.tasks.tissue.csd_aodf_nufid(data_imap, pve_internal, tracking_params)

full path to a nifti file containing the CSD Number of fiber directions (nufid) map [1]

References

[1] C. Poirier and M. Descoteaux,

“Filtering Methods for Asymmetric ODFs: Where and How Asymmetry Occurs in the White Matter.” bioRxiv. 2022 Jan 1; 2022.12.18.520881. doi: https://doi.org/10.1101/2022.12.18.520881

AFQ.tasks.tissue.get_tissue_plan(kwargs)