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ReportCO2inhalCvr brick

Generates the report for CVR evaluation using hypercapnia challenge pipeline

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
  

• regressor_physio (a string representing an existing file)

  Time series data that represent the physiological processes (ETCO2) thought to contribute to the CVR in the fMRI signal (valid extensions: .mat).

  ex. /home/username/data/derived_data/patient_ref_data/CVR_physio_reg.mat
  

• beta_image (a string representing an existing file)

  The estimated effect size or regression coefficients associated with the 1st predictor (e.g., conditions or regressors) included in the GLM model. A spatial map that represent the estimated effect size or intensity of activation/deactivation associated with the 1st predictor/regressor at each voxel in the brain (valid extensions:.nii)

  ex. /home/username/data/derived_data/patient_ref_data/beta_0001.nii
  

• beta_cmap (a string, optional)

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

  ex. rainbow
  

• beta_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>
  

• beta_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>
  

• spmT_image (a string representing an existing file)

  A file containing t-statistic values per voxel, which indicate the strength of the effect of interest at each brain voxel, derived from the general linear model (GLM) analysis performed in SPM (valid extensions:.nii)

  ex. /home/username/data/derived_data/patient_ref_data/spmT_0001.nii
  

• spmT_cmap (a string, optional)

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

  ex. rainbow
  

• spmT_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>
  

• spmT_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>
  

• patient_info

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

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

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