Outputs of MIALSRTK BIDS App¶

Processed, or derivative, data are outputed to <bids_dataset/derivatives>/ and follow the BIDS v1.4.1 standard (see BIDS Derivatives) whenever possible.

BIDS derivatives entities¶

Entity	Description
`sub-<label>`	Distinguish different subjects
`ses-<label>`	Distinguish different T2w scan acquisition sessions
`run-<label>`	Distinguish different T2w scans
`rec-<label>`	Distinguish images reconstructed using scattered data interpolation (SDI) or super-resolution (SR) methods
`id-<label>`	Distinguish outputs of reconstructions run multiple times with different configuration

See Original BIDS Entities Appendix for more description.

Note

A new entity id- has been introduced to distinguish between outputs when the pipeline is run with multiple configurations (such a new order of scans) on the same subject.

Main MIALSRTK BIDS App Derivatives¶

Main outputs produced by MIALSRTK BIDS App are written to <bids_dataset/derivatives>/pymialsrtk-<variant>/sub-<label>/(_ses-<label>/). The execution log of the full workflow is saved as sub-<label>(_ses-<label>)_id-<label>_log.txt`.

Anatomical derivatives¶

Anatomical derivatives are placed in each subject’s anat/ subfolder, including:
- The brain masks of the T2w scans:
  anat/sub-<label>(_ses-<label>)_run-01_id-<label>_desc-brain_mask.nii.gz
  
  anat/sub-<label>(_ses-<label>)_run-02_id-<label>_desc-brain_mask.nii.gz
  
  anat/sub-<label>(_ses-<label>)_run-03_id-<label>_desc-brain_mask.nii.gz
  
  …
- The preprocessed T2w scans used for slice motion estimation and scattered data interpolation (SDI) reconstruction:
  anat/sub-<label>(_ses-<label>)_run-01_id-<label>_desc-preprocSDI_T2w.nii.gz
  
  anat/sub-<label>(_ses-<label>)_run-02_id-<label>_desc-preprocSDI_T2w.nii.gz
  
  anat/sub-<label>(_ses-<label>)_run-03_id-<label>_desc-preprocSDI_T2w.nii.gz
  
  …
- The preprocessed T2w scans used for super-resolution reconstruction:
  anat/sub-<label>(_ses-<label>)_run-01_id-<label>_desc-preprocSR_T2w.nii.gz
  
  anat/sub-<label>(_ses-<label>)_run-02_id-<label>_desc-preprocSR_T2w.nii.gz
  
  anat/sub-<label>(_ses-<label>)_run-03_id-<label>_desc-preprocSR_T2w.nii.gz
  
  …
- The high-resolution image reconstructed by SDI:
  anat/sub-<label>(_ses-<label>)_rec-SDI_id-<label>_T2w.nii.gz
  
  anat/sub-<label>(_ses-<label>)_rec-SDI_id-<label>_T2w.json
- The high-resolution image reconstructed by SDI:
  anat/sub-<label>(_ses-<label>)_rec-SR_id-<label>_T2w.nii.gz
  
  anat/sub-<label>(_ses-<label>)_rec-SR_id-<label>_T2w.json
The slice-by-slice transforms of all T2W scans estimated during slice motion estimation and SDI reconstruction and used in the super-resolution forward model are placed in each subject’s xfm/ subfolder:
- xfm/sub-<label>(_ses-<label>)_run-1_id-<label>_T2w_from-origin_to-SDI_mode-image_xfm.txt
- xfm/sub-<label>(_ses-<label>)_run-2_id-<label>_T2w_from-origin_to-SDI_mode-image_xfm.txt
- xfm/sub-<label>(_ses-<label>)_run-3_id-<label>_T2w_from-origin_to-SDI_mode-image_xfm.txt
- …

Nipype Workflow Derivatives¶

The execution of the Nipype workflow (pipeline) involves the creation of a number of intermediate outputs for each subject sub- and each run rec- which are written to <bids_dataset/derivatives>/nipype/sub-<label>/rec-<id_label>/srr_pipeline where <id_label> corresponds to the label used previously for the entity id-:

To enhance transparency on how data is processed, outputs include a pipeline execution graph saved as srr_pipeline/graph.png which summarizes all processing nodes involves in the given processing pipeline:

Execution details (data provenance) of each interface (node) of a given pipeline are reported in srr_pipeline/<interface_name>/_report/report.rst