ReportAnatMriqc brick¶

Generates the report for anatomical data in mriqc pipeline¶

Mandatory inputs parameters:

anat (a string representing an existing file)
Input anat image (valid extensions: [.nii, .nii.gz]).
ex. '/home/username/data/raw_data/T1w.nii'
IQMs_file (a string representing an existing file)
A .json file containing the IQMs (valid extensions: [.json]).
ex. '/home/username/data/derived_data/T1w_anat_qc.json'
art_mask (a pathlike object or string representing a file)
Artifact mask image (extensions: [.nii, .nii.gz]).
ex. '/home/username/data/derived_data/art_T1w_mask.nii'
air_mask (a pathlike object or string representing a file)
Air mask (“hat” mask without artifacts) image.
ex. '/home/username/data/derived_data/air_T1w_mask.nii'

brain_mask (a string representing an existing file)

Mask image.

ex. '/home/username/data/derived_data/pre_n4c_T1W_clipped_desc-brain.nii'

head_mask (a pathlike object or string representing a file)
Outskin mask (extensions: [.nii, .nii.gz])
ex. '/home/username/data/derived_data/T1w_brain_outskin_mask.nii'
segmentation (a string representing an existing file)
Segmentation mask (valid extensions: [.nii, .nii.gz]).
ex. '/home/username/data/derived_data/ss_n4c_T1w_clippep_seg.nii'

Optional inputs with default value parameters:

anat_fig_cols (an integer, optional, default value is 5)
The number of columns for the anatomical slice planes plot.
ex. 5
anat_fig_rows (an integer, optional, default value is 5)
The number of lines for the anatomical slice planes plot.
ex. 5
out_prefix (a string, optional, default value is ‘spikes’)
Prefix of the output image.
ex. 'spikes_'
norm_anat (a string representing an existing file)
An existing, uncompressed normalised anatomical image file (valid extensions: [.nii, .nii.gz]).
ex. '/home/username/data/raw_data/T1w.nii'
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_fig_rows (an integer, optional, default value is 5)
The number of lines for the normalised anatomical slice planes plot.
ex. 5

Optional inputs:

anat_inf_slice_start (an integer, optional)
The first index displayed in anatomical slice planes plot. Default is Undefined (ie parameter not used).
ex. 0
anat_slices_gap (an integer, optional)
Gap between slices in anatomical slice planes plot. Default is Undefined (ie parameter not used).
ex. 0
norm_anat_inf_slice_start (an integer, optional)
The first index displayed in normalised anatomical slice planes plot. Default is Undefined (ie parameter not used).
ex. 0
norm_anat_slices_gap (an integer, optional)
Gap between slices in normalised anatomical slice planes plot. Default is Undefined (ie parameter not used).
ex. 0

Outputs parameters:

report (a strings representing a file)

The generated report (pdf).

ex. '/home/username/data/derived_data/T1w_ref_anatomical_mriqcReport_2023_03_31_11_42_10_75.pdf'

Useful links: