qsirecon.workflows.recon.mrtrix module
MRTrix workflows
Note that in nipype interfaces the threading-controlling attribute is
nthreads, not the typical num_threads expected by nipype.
To keep threading consistent between nipype and mrtrix, the
nthreads attribute needs to be set in the interface and the
n_procs attribute needs to be set on the Node.
- qsirecon.workflows.recon.mrtrix.init_global_tractography_wf(inputs_dict, name='mrtrix_recon', qsirecon_suffix='', params={})[source]
Run multi-shell, multi-tissue global tractography
This workflow uses mrtrix tools to run csd on multishell data.
Inputs
- dwi_file
Preprocessed DWI series
- wm_txt
SH fiber response function for white matter
- gm_txt
SH fiber response function for gray matter
- csf_txt
SH fiber response function for CSF
Outputs
- global_wm_fod
FOD SH image enhanced by global tractography
- global_iso_fod
FOD SH coefficients for other tissue compartments.
- l1_penalty
the residual data energy image, including the L1-penalty imposed by the particle potential
- qsirecon.workflows.recon.mrtrix.init_mrtrix_connectivity_wf(inputs_dict, name='mrtrix_connectivity', params={}, qsirecon_suffix='')[source]
Runs
tck2connectomeon atckfile.Inputs
- tck_file
mrtrix3 tck file.
Outputs
- matfile
A MATLAB-format file with numerous connectivity matrices for each atlas.
- qsirecon.workflows.recon.mrtrix.init_mrtrix_csd_recon_wf(inputs_dict, name='mrtrix_recon', qsirecon_suffix='', params={})[source]
Create FOD images for WM, GM and CSF.
This workflow uses mrtrix tools to run csd on multishell data. At the end, mtnormalise is run.
Inputs
Default qsirecon inputs
- qsiprep_5tt_hsvs
A hybrid surface volume segmentation 5tt image aligned with the QSIRecon T1w
Outputs
- wm_txt
SH fiber response function for white matter
- wm_fod
FOD SH coefficients for white matter
- gm_txt
SH fiber response function for gray matter
- gm_fod
FOD SH coefficients for gray matter
- csf_txt
SH fiber response function for CSF
- csf_fod
FOD SH coefficients for CSF
- fod_sh_mif
The same file as wm_fod.
Params
- response: dict
parameters for estimating the response function. A minimal example would be
{"algorighm": "dhollander"}- fod: dict
parameters for dwi2fod. A minimal example would be
{"algorithm": "msmt_csd", "max_sh": [6, 8, 8]}.- mtnormalize: bool
Should the FODs be mtnormalized?
- qsirecon.workflows.recon.mrtrix.init_mrtrix_tractography_wf(inputs_dict, name='mrtrix_tracking', qsirecon_suffix='', params={})[source]
Run tractography
This workflow uses mrtrix tools to run csd on multishell data.
Inputs
- fod_sh_mif
mif file containing spherical harmonics for tractography
Outputs
- global_wm_fod
FOD SH image enhanced by global tractography
- global_iso_fod
FOD SH coefficients for other tissue compartments.
- l1_penalty
the residual data energy image, including the L1-penalty imposed by the particle potential