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ReportPerfDsc brick

Generates report for Perfusion study using DSC-MRI

Inputs parameters:

• norm_anat (a string representing an existing file)

  Normalised anatomical image (valid extensions: [.nii, .nii.gz]).

  ex. '/home/username/data/raw_data/wAnat.nii'
  

• norm_anat_fig_rows (an integer, optional, default value is 5)

  The number of lines for the normalised anatomical slice planes plot.

  ex. 5
  

• norm_anat_fig_cols (an integer, optional, default value is 5)

  The number of columns for the normalised anatomical slice planes plot.

  ex. 5
  

• norm_anat_inf_slice_start (an integer, optional)

  The first index displayed in the normalised anatomical slice planes plot. Default is Undefined (ie automatically determined).

  ex. 10
  

• norm_anat_slices_gap (an integer, optional)

  Gap between slices in normalised anatomical slice planes plot. Default is Undefined (ie automatically determined).

  ex. 13
  

• norm_anat_cmap (a string, optional)

  The name of the colors range that are used for the normalised anatomical slice planes plot (default is Greys_r).

  ex. Greys_r
  

• norm_anat_vmin (a float, optional)

  Specifies the minimum value of the data range to be mapped to the colormap. Any value lower than vmin will be clipped to vmin before mapping to colors.

  ex. <undefined>
  

• norm_anat_vmax (a float, optional)

  Specifies the maximum value of the data range to be mapped to the colormap. Any value higher than vmax will be clipped to vmax before mapping to colors.

  ex. <undefined>
  

• norm_func (a string representing an existing file)

  Normalised functional image (valid extensions: [.nii, .nii.gz]).

  ex. '/home/username/data/derived_data/wrFunc.nii'
  

• norm_func_fig_rows (an integer, optional, default value is 5)

  The number of lines for the normalised functional slice planes plot.

  ex. 5
  

• norm_func_fig_cols (an integer, optional, default value is 5)

  The number of columns for the normalised functional slice planes plot.

  ex. 5
  

• norm_func_inf_slice_start (an integer, optional)

  The first index displayed in the normalised functional slice planes plot. Default is Undefined (ie automatically determined).

  ex. <undefined>
  

• norm_func_slices_gap (an integer, optional)

  Gap between slices in normalised functional slice planes plot. Default is Undefined (ie automatically determined).

  ex. <undefined>
  

• norm_func_cmap (a string, optional)

  The name of the colors range that are used for the normalised functional slice planes plot (default is Greys_r).

  ex. Greys_r
  

• norm_func_vmin (a float, optional)

  Specifies the minimum value of the data range to be mapped to the colormap. Any value lower than vmin will be clipped to vmin before mapping to colors.

  ex. <undefined>
  

• norm_func_vmax (a float, optional)

  Specifies the maximum value of the data range to be mapped to the colormap. Any value higher than vmax will be clipped to vmax before mapping to colors.

  ex. <undefined>
  

• realignment_parameters (a string representing an existing file)

  Estimated translation and rotation parameters during fMRI recording (valid extensions: .txt).

  ex. /home/username/data/derived_data/rp_Func.txt
  

• CBV_image (a string representing an existing file)

  Cerebral Blood Volume map (a file with .nii format).

  ex. /home/username/data/derived_data/Func_CBV_deconv.nii
  

• CBV_cmap (a string, optional)

  The name of the colors range that are used for the CBV map slice planes plot (default: rainbow).

  ex. rainbow
  

• CBV_vmin (a float, optional)

  Specifies the minimum value of the data range to be mapped to the colormap. Any value lower than vmin will be clipped to vmin before mapping to colors.

  ex. <undefined>
  

• CBV_vmax (a float, optional)

  Specifies the maximum value of the data range to be mapped to the colormap. Any value higher than vmax will be clipped to vmax before mapping to colors.

  ex. <undefined>
  

• CBF_image (a string representing an existing file)

  Cerebral Blood Flow map (a file with .nii format).

  ex. /home/username/data/derived_data/Func_CBF_deconv.nii
  

• CBF_cmap (a string, optional)

  The name of the colors range that are used for the CBF map slice planes plot (default: rainbow).

  ex. rainbow
  

• CBF_vmin (a float, optional)

  Specifies the minimum value of the data range to be mapped to the colormap. Any value lower than vmin will be clipped to vmin before mapping to colors.

  ex. <undefined>
  

• CBF_vmax (a float, optional)

  Specifies the maximum value of the data range to be mapped to the colormap. Any value higher than vmax will be clipped to vmax before mapping to colors.

  ex. <undefined>
  

• Tmax_image (a string representing an existing file)

  The Time to Maximum map (a file with .nii format).

  ex. /home/username/data/derived_data/Func_Tmax_deconv.nii
  

• Tmax_cmap (a string, optional)

  The name of the colors range that are used for the Tmax map slice planes plot (default: rainbow).

  ex. rainbow
  

• Tmax_vmin (a float, optional)

  Specifies the minimum value of the data range to be mapped to the colormap. Any value lower than vmin will be clipped to vmin before mapping to colors.

  ex. <undefined>
  

• Tmax_vmax (a float, optional)

  Specifies the maximum value of the data range to be mapped to the colormap. Any value higher than vmax will be clipped to vmax before mapping to colors.

  ex. <undefined>
  

• MTT_image (a string representing an existing file)

  Mean Transit Time map (a file with .nii format).

  ex. /home/username/data/derived_data/Func_MTT_deconv.nii
  

• MTT_cmap (a string, optional)

  The name of the colors range that are used for the MTT map slice planes plot (default: rainbow).

  ex. rainbow
  

• MTT_vmin (a float, optional)

  Specifies the minimum value of the data range to be mapped to the colormap. Any value lower than vmin will be clipped to vmin before mapping to colors.

  ex. <undefined>
  

• MTT_vmax (a float, optional)

  Specifies the maximum value of the data range to be mapped to the colormap. Any value higher than vmax will be clipped to vmax before mapping to colors.

  ex. <undefined>
  

• aif_file

  The AIF (a file in .json format) typically obtained previously with the Make_AIF brick.

  ex. '/home/username/data/raw_data/swrfunc_aif.json'
  

• patient_info

  Optional dictionary with information about the patient (keys in [‘PatientRef’, ‘Pathology’, ‘Age’, ‘Sex’, MR’])

  ex. {'PatientRef': 'sub-1', 'Pathology': 'ACMD', 'Age': '56', 'Sex': 'M', 'MR': '3T'}
  

Outputs parameters:

• report (a strings representing a file)

  The generated report (pdf).

  ex. /home/username/data/derived_data/sub-1_CO2_inhal_CVR_Report_2024_01_24_09_34_58_08.pdf