qsiprep.interfaces.shoreline module

SHORELine interfaces

class qsiprep.interfaces.shoreline.B0Mean(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Mandatory Inputs:

b0_images (a list of items which are a pathlike object or string representing an existing file)

Outputs:

average_image (a pathlike object or string representing an existing file)

class qsiprep.interfaces.shoreline.CalculateCNR(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Optional Inputs:

  • hmc_warped_images (a list of items which are a pathlike object or string representing an existing file)

  • mask_image (a pathlike object or string representing an existing file)

  • predicted_images (a list of items which are a pathlike object or string representing an existing file)

Outputs:

cnr_image (a pathlike object or string representing an existing file)

class qsiprep.interfaces.shoreline.ExtractDWIsForModel(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Take a DWI series with interspersed b0 images and create a model-ready version

Optional Inputs:

  • b0_indices (a list of items which are any value)

  • bval_files (a list of items which are a pathlike object or string representing an existing file)

  • bvec_files (a list of items which are a pathlike object or string representing an existing file)

  • dwi_files (a list of items which are a pathlike object or string representing an existing file)

  • transforms (a list of items which are any value)

Outputs:

  • model_bvals (a list of items which are a pathlike object or string representing an existing file)

  • model_bvecs (a list of items which are a pathlike object or string representing an existing file)

  • model_dwi_files (a list of items which are a pathlike object or string representing an existing file)

  • transforms (a list of items which are any value)

class qsiprep.interfaces.shoreline.IterationSummary(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SummaryInterface

Optional Inputs:

collected_motion_files (a list of items which are a pathlike object or string representing an existing file)

Outputs:

  • iteration_summary_file (a pathlike object or string representing an existing file)

  • plot_file (a pathlike object or string representing an existing file)

class qsiprep.interfaces.shoreline.ReorderOutputs(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Mandatory Inputs:

  • b0_indices (a list of items which are any value)

  • b0_mean (a pathlike object or string representing an existing file)

  • initial_transforms (a list of items which are a pathlike object or string representing an existing file)

  • model_based_transforms (a list of items which are a list of items which are any value)

  • model_predicted_images (a list of items which are a pathlike object or string representing an existing file)

  • warped_b0_images (a list of items which are a pathlike object or string representing an existing file)

  • warped_dwi_images (a list of items which are a pathlike object or string representing an existing file)

Outputs:

  • full_predicted_dwi_series (a list of items which are a pathlike object or string representing an existing file)

  • full_transforms (a list of items which are a list of items which are any value)

  • hmc_warped_images (a list of items which are a pathlike object or string representing an existing file)

class qsiprep.interfaces.shoreline.SHORELineReport(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SummaryInterface

Optional Inputs:

  • iteration_summary (a pathlike object or string representing an existing file)

  • model_predicted_images (a list of items which are a pathlike object or string representing an existing file)

  • original_images (a list of items which are a pathlike object or string representing an existing file)

  • registered_images (a list of items which are a pathlike object or string representing an existing file)

Outputs:

  • out_report (a pathlike object or string representing an existing file) – HTML segment containing summary.

  • plot_file (a pathlike object or string representing an existing file)

class qsiprep.interfaces.shoreline.SignalPrediction(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Mandatory Inputs:

  • aligned_b0_mean (a pathlike object or string representing an existing file)

  • aligned_mask (a pathlike object or string representing an existing file)

Optional Inputs:

  • aligned_bvecs (a list of items which are a pathlike object or string representing an existing file or an array)

  • aligned_dwis (a list of items which are a pathlike object or string representing an existing file)

  • bval_to_predict (a float)

  • bvals (a list of items which are a pathlike object or string representing an existing file or an array)

  • bvec_to_predict (an array)

  • minimal_q_distance (a float) – (Nipype default value: 2.0)

  • model (a string) – (Nipype default value: 3dSHORE)

Outputs:

predicted_image (a pathlike object or string representing an existing file)

qsiprep.interfaces.shoreline.before_after_images(orig_file, aligned_file, model_file, imagenum)[source]
qsiprep.interfaces.shoreline.quick_load_images(image_list, dtype=<class 'numpy.float32'>)[source]
qsiprep.interfaces.shoreline.scaled_mip(img1, img2, img3, axis)[source]
qsiprep.interfaces.shoreline.to_image(fig)[source]