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