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DOC: update outputs.rst [skip ci]
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sebastientourbier committed Nov 5, 2020
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Expand Up @@ -7,44 +7,70 @@ Processed, or derivative, data are outputed to ``<bids_dataset/derivatives>/``.
Main MIALSRTK BIDS App Derivatives
==========================================

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

.. note:: MIALSRTK BIDS App outputs follows the :abbr:`BIDS (brain imaging data structure)` Derivatives specification (see `BIDS Derivatives Extension <https://bids-specification.readthedocs.io/en/v1.4.0/>`_) whenever possible. However a new entity ``id-<srr_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.

BIDS derivatives entities
--------------------------

.. tabularcolumns:: |l|c|p{5cm}|

+--------------+------------------+-------------------------------------------------------+
| **Entity** | **Label** | **Description** |
+--------------+------------------+-------------------------------------------------------+
| ``sub`` | <subject_label> | Label of the subject |
+--------------+------------------+-------------------------------------------------------+
| ``ses`` | <session_label> | Label of the session |
+--------------+------------------+-------------------------------------------------------+
| ``run`` | <run_label> | Label of the T2w scan |
+--------------+------------------+-------------------------------------------------------+
| ``rec`` | <recon_label> | Label of the reconstruction type |
+--------------+------------------+-------------------------------------------------------+
| ``id`` | <srr_id> | Label of the reconstruction for a given configuration |
+--------------+------------------+-------------------------------------------------------+

Anatomical derivatives
------------------------
* Anatomical derivatives are placed in each subject's ``anat/`` subfolder, including:

* The brain masks of the T2w scans:
* The brain masks of the T2w scans:

- ``anat/sub-<subject_label>_run-01_desc-brain_mask.nii.gz``
- ``anat/sub-<subject_label>_run-02_desc-brain_mask.nii.gz``
- ``anat/sub-<subject_label>_run-03_desc-brain_mask.nii.gz``
- ``anat/sub-<subject_label>(_ses-<session_label>)_run-01_id-<srr_id>_desc-brain_mask.nii.gz``
- ``anat/sub-<subject_label>(_ses-<session_label>)_run-02_id-<srr_id>_desc-brain_mask.nii.gz``
- ``anat/sub-<subject_label>(_ses-<session_label>)_run-03_id-<srr_id>_desc-brain_mask.nii.gz``
- ...

* The preprocessed T2w scans used for slice motion estimation and scattered data interpolation (SDI) reconstruction:

- ``anat/sub-<subject_label>_run-01_desc-SDIprep_T2w.nii.gz``
- ``anat/sub-<subject_label>_run-02_desc-SDIprep_T2w.nii.gz``
- ``anat/sub-<subject_label>_run-03_desc-SDIprep_T2w.nii.gz``
- ``anat/sub-<subject_label>(_ses-<session_label>)_run-01_id-<srr_id>_desc-preprocSDI_T2w.nii.gz``
- ``anat/sub-<subject_label>(_ses-<session_label>)_run-02_id-<srr_id>_desc-preprocSDI_T2w.nii.gz``
- ``anat/sub-<subject_label>(_ses-<session_label>)_run-03_id-<srr_id>_desc-preprocSDI_T2w.nii.gz``
- ...

* The preprocessed T2w scans used for super-resolution reconstruction:

- ``anat/sub-<subject_label>_run-01_desc-SRprep_T2w.nii.gz``
- ``anat/sub-<subject_label>_run-02_desc-SRprep_T2w.nii.gz``
- ``anat/sub-<subject_label>_run-03_desc-SRprep_T2w.nii.gz``
- ``anat/sub-<subject_label>(_ses-<session_label>)_run-01_id-<srr_id>_desc-preprocSR_T2w.nii.gz``
- ``anat/sub-<subject_label>(_ses-<session_label>)_run-02_id-<srr_id>_desc-preprocSR_T2w.nii.gz``
- ``anat/sub-<subject_label>(_ses-<session_label>)_run-03_id-<srr_id>_desc-preprocSR_T2w.nii.gz``
- ...



* The high-resolution image reconstructed by SDI:

- ``anat/sub-01_rec-SDI_id-1_T2w.nii.gz``
- ``anat/sub-01_rec-SDI_id-1_T2w.json``
- ``anat/sub-<subject_label>(_ses-<session_label>)_rec-SDI_id-<srr_id>_T2w.nii.gz``
- ``anat/sub-<subject_label>(_ses-<session_label>)_rec-SDI_id-<srr_id>_T2w.json``

* The high-resolution image reconstructed by SDI:

- ``anat/sub-01_rec-SR_id-1_T2w.nii.gz``
- ``anat/sub-01_rec-SR_id-1_T2w.json``
- ``anat/sub-<subject_label>(_ses-<session_label>)_rec-SR_id-<srr_id>_T2w.nii.gz``
- ``anat/sub-<subject_label>(_ses-<session_label>)_rec-SR_id-<srr_id>_T2w.json``

* The slice-to-volume registration transform of each 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-<subject_label>(_ses-<session_label>)_run-1_id-<srr_id>_T2w_from-origin_to-SDI_mode-image_xfm.txt``
- ``xfm/sub-<subject_label>(_ses-<session_label>)_run-2_id-<srr_id>_T2w_from-origin_to-SDI_mode-image_xfm.txt``
- ``xfm/sub-<subject_label>(_ses-<session_label>)_run-3_id-<srr_id>_T2w_from-origin_to-SDI_mode-image_xfm.txt``
- ...

Nipype Workflow Derivatives
==========================================
Expand All @@ -66,5 +92,3 @@ Execution details (data provenance) of each interface (node) of a given pipeline
.. image:: images/nipype_node_report.png
:width: 888
:align: center

.. note:: MIALSRTK BIDS App outputs are currently being updated to conform to the :abbr:`BIDS (brain imaging data structure)` Derivatives specification (see `BIDS Derivatives Extension <https://bids-specification.readthedocs.io/en/v1.4.0/>`_).

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