Analysis¶
Module contents¶
Preconfigured analyses and pipelines to be used with django_analyses.
Example
To import the analyses and pipelines to the database, start a Django shell session and run:
from django_mri.analysis.utils import load_mri_analyses
load_mri_analyses()
See also
Subpackages¶
Submodules¶
django_mri.analysis.analysis_definitions module¶
django_mri.analysis.mri_interfaces module¶
Each analysis version imported to the database using django_analyses needs to
have a matching interface registered for it in the project’s settings. This
interface is expected to be some class exposing a method (by default
run()) which returns a dictionary of outputs matching its associated
OutputSpecification.
References
-
django_mri.analysis.mri_interfaces.interfaces= {'BET': {None: <class 'nipype.interfaces.fsl.preprocess.BET'>}, 'CAT12 Segmentation': {'12.6': <class 'django_mri.analysis.interfaces.matlab.spm.cat12.segmentation.segmentation.Segmentation'>}, 'FAST': {<property object>: <class 'django_mri.analysis.interfaces.fsl.fast.FastWrapper'>}, 'FLIRT': {None: <class 'nipype.interfaces.fsl.preprocess.FLIRT'>}, 'FNIRT': {None: <class 'nipype.interfaces.fsl.preprocess.FNIRT'>}, 'FSL Anatomical Processing Script': {'BETA': <class 'django_mri.analysis.interfaces.fsl.fsl_anat.FslAnat'>}, 'ReconAll': {None: <class 'nipype.interfaces.freesurfer.preprocess.ReconAll'>}, 'SUSAN': {None: <class 'nipype.interfaces.fsl.preprocess.SUSAN'>}, 'apply_topup': {None: <class 'nipype.interfaces.fsl.epi.ApplyTOPUP'>}, 'bias_correct': {None: <class 'nipype.interfaces.mrtrix3.preprocess.DWIBiasCorrect'>}, 'binary_maths': {None: <class 'nipype.interfaces.fsl.maths.BinaryMaths'>}, 'degibbs': {None: <class 'nipype.interfaces.mrtrix3.preprocess.MRDeGibbs'>}, 'denoise': {None: <class 'nipype.interfaces.mrtrix3.preprocess.DWIDenoise'>}, 'dwipreproc': {'BETA': <class 'django_mri.analysis.interfaces.mrtrix3.dwifslpreproc.DwiFslPreproc'>}, 'eddy': {None: <class 'nipype.interfaces.fsl.epi.Eddy'>}, 'fslmerge': {None: <class 'nipype.interfaces.fsl.utils.Merge'>}, 'fslreorient2std': {None: <class 'nipype.interfaces.fsl.utils.Reorient2Std'>}, 'fslroi': {None: <class 'nipype.interfaces.fsl.utils.ExtractROI'>}, 'mean_image': {None: <class 'nipype.interfaces.fsl.maths.MeanImage'>}, 'robustfov': {None: <class 'nipype.interfaces.fsl.utils.RobustFOV'>}, 'topup': {<property object>: <class 'django_mri.analysis.interfaces.fsl.topup.TopupWrapper'>}}¶ A dictionary that should be imported in the project’s settings and included within the ANALYSIS_INTERFACES setting.
django_mri.analysis.messages module¶
A module storing strings used to display messages.