ReportFuncMriqc brick¶

Generates the report for functional data in mriqc pipeline¶

Mandatory inputs parameters:

func (a string representing an existing file)
Input functional image (valid extensions: [.nii, .nii.gz]).
ex. '/home/username/data/raw_data/func.nii'
IQMs_file (a string representing an existing file)
A .json file containing the IQMs (valid extensions: [.json]).
ex. '/home/username/data/derived_data/func_func_qc.json'

Optional inputs with default value parameters:

func_fig_cols (an integer, optional, default value is 5)
The number of columns for the functional slice planes plot.
ex. 5
func_fig_rows (an integer, optional, default value is 5)
The number of lines for the functional slice planes plot.
ex. 5
out_prefix (a string, optional, default value is ‘spikes’)
Prefix of the output image.
ex. 'spikes_'
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_fig_rows (an integer, optional, default value is 5)
The number of lines for the normalised functional slice planes plot.
ex. 5

Optional inputs:

brain_mask (a string representing an existing file)

Mask image.

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

func_inf_slice_start (an integer, optional)
The first index displayed in functional slice planes plot. Default is Undefined (ie parameter not used).
ex. 0
func_slices_gap (an integer, optional)
Gap between slices in functional slice planes plot. Default is Undefined (ie parameter not used).
ex. 0
IQMs_plot (a string representing an existing file)
A figure with carpet and outliers/dvars/FD/spikes plot.
ex. '/home/username/data/raw_data/func_valid_fmriplot.png'
norm_func (a string representing an existing file)
An existing, normalised functional image file (valid extensions: [.nii, .nii.gz]).
ex. '/home/username/data/raw_data/w_n4c_mean_reg_func_valid.nii'
mean_func (a string representing an existing file)
Mean functional image file (valid extensions: [.nii, .nii.gz]).
ex. '/home/username/data/raw_data/mean_reg_func_valid.nii'
norm_func_inf_slice_start (an integer, optional)
The first index displayed in normalised functional slice planes plot. Default is Undefined (ie parameter not used).
ex. 0
norm_func_slices_gap (an integer, optional)
Gap between slices in normalised functional slice planes plot. Default is Undefined (ie parameter not used).
ex. 0
stddev_func (a string representing an existing file)
Functional standard deviation image (valid extensions: [.nii, .nii.gz]).
ex. '/home/username/data/raw_data/reg_func_valid_stddev.nii'

Outputs parameters:

report (a strings representing a file)

The generated report (pdf).

ex. ''/home/username/data/derived_data/func_ref_functional_mriqcReport_2023_03_31_11_42_10_75.pdf'

Useful links: