qsirecon.interfaces.reports module

Interfaces to generate reportlets

class qsirecon.interfaces.reports.AboutSummary(from_file=None, resource_monitor=None, **inputs)

Bases: SummaryInterface

Optional Inputs:

• command (a string) – QSIRecon command.

• version (a string) – QSIRecon version.

Outputs:

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

class qsirecon.interfaces.reports.CLIReconPeaksReport(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: CommandLine

Wrapped executable: recon_plot.

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• background_image (a pathlike object or string representing an existing file) – Maps to a command-line argument: --background_image %s.

• directions_file (a pathlike object or string representing an existing file) – Maps to a command-line argument: --directions %s.

• environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

• fib_file (a pathlike object or string representing an existing file) – Maps to a command-line argument: --fib %s.

• mask_file (a pathlike object or string representing an existing file) – Maps to a command-line argument: --mask_file %s.

• mif_file (a pathlike object or string representing an existing file) – Maps to a command-line argument: --mif %s.

• odf_file (a pathlike object or string representing an existing file) – Maps to a command-line argument: --amplitudes %s.

• odf_report (a pathlike object or string representing a file) – Maps to a command-line argument: --odfs_image %s. (Nipype default value: odfs_mosaic.png)

• odf_rois (a pathlike object or string representing an existing file) – Maps to a command-line argument: --odf_rois %s.

• peak_report (a pathlike object or string representing a file) – Maps to a command-line argument: --peaks_image %s. (Nipype default value: peaks_mosaic.png)

• peaks_only (a boolean) – Only produce a peak directions report. Maps to a command-line argument: --peaks_only. (Nipype default value: False)

• subtract_iso (a boolean) – Subtract isotropic component from ODFs. Maps to a command-line argument: --subtract-iso. (Nipype default value: False)

Outputs:

• odf_report (a pathlike object or string representing a file)

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

class qsirecon.interfaces.reports.ConnectivityReport(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Optional Inputs:

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

Outputs:

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

class qsirecon.interfaces.reports.InteractiveReport(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

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

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

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

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

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

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

• series_qc_file (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.

class qsirecon.interfaces.reports.ScalarReport(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Plot scalar maps in a matrix of images.

Mandatory Inputs:

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

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

• scalar_metadata (a list of items which are a dictionary with keys which are any value and with values which are any value)

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

Optional Inputs:

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

Outputs:

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

class qsirecon.interfaces.reports.SubjectSummary(from_file=None, resource_monitor=None, **inputs)

Bases: SummaryInterface

Optional Inputs:

• dwi (a list of items which are a pathlike object or string representing an existing file or a list of items which are a pathlike object or string representing an existing file) – Preprocessed DWI series.

• nstd_spaces (a list of items which are a string) – List of non-standard spaces.

• std_spaces (a list of items which are a string) – List of standard spaces.

• subject_id (a string) – Subject ID.

• subjects_dir (a pathlike object or string representing a directory or None) – FreeSurfer subjects directory.

• t1w (a list of items which are a pathlike object or string representing an existing file) – T1w structural images.

• t2w (a list of items which are a pathlike object or string representing an existing file) – T2w structural images.

Outputs:

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

• subject_id (a string) – FreeSurfer subject ID.

class qsirecon.interfaces.reports.SummaryInterface(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Outputs:

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

qsirecon.interfaces.reports.plot_scalar_map(underlay, overlay, mask, title, z_cuts, axes, dseg=None, vmin=None, vmax=None, cmap='Reds')

Plot a scalar map with a histogram of the voxel-wise values.