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DOC: Update outputs.rst with new BIDS naming convention [skip ci]
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sebastientourbier committed Mar 4, 2021
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Expand Up @@ -16,7 +16,11 @@ BIDS derivatives entities
+--------------------------+------------------------------------------------------------------------------------------------------------+
| ``ses-<label>`` | Distinguish different acquisition sessions |
+--------------------------+------------------------------------------------------------------------------------------------------------+
| ``label-<label>`` | Describe the type of brain tissue segmented (for _probseg/dseg) or the parcellation atlas (for _atlas) |
| ``label-<label>`` | Describe the type of brain tissue segmented (for _probseg/dseg) |
+--------------------------+------------------------------------------------------------------------------------------------------------+
| ``atlas-<label>`` | Distinguish data derived from different types of parcellation atlases |
+--------------------------+------------------------------------------------------------------------------------------------------------+
| ``res-<label>`` | Distinguish data derived from the different scales of Lausanne2008 and Lausanne2018 parcellation atlases |
+--------------------------+------------------------------------------------------------------------------------------------------------+
| ``space-DWI`` | Distinguish anatomical MRI derivatives in the target diffusion MRI space |
+--------------------------+------------------------------------------------------------------------------------------------------------+
Expand All @@ -25,7 +29,9 @@ BIDS derivatives entities

See `Original BIDS Entities Appendix <https://bids-specification.readthedocs.io/en/v1.4.1/99-appendices/09-entities.html>`_ for more description.

.. note:: A new suffix `_atlas` has been introduced, that is used in combination with the ``label-<atlas_label>`` entity (where ``<atlas_label>``:``Desikan``/``L2008``/``L2018``) to distinguish different parcellation atlas outputs.
.. note:: A new BIDS entity `atlas-<atlas_label>` (where ``<atlas_label>``: ``Desikan``/ ``L2008``/ ``L2018``) has been introduced, that is used in combination
with the ``res-<atlas_scale>`` (where ``<atlas_scale>``: ``scale1`` / ``scale2`` / ``scale3`` / ``scale4`` / ``scale5``) entity to distinguish
data derived from different parcellation atlases and different scales.


Main Connectome Mapper Derivatives
Expand Down Expand Up @@ -54,14 +60,19 @@ Anatomical derivatives

* The five different brain parcellations:

- ``anat/sub-<subject_label>_label-L2018_desc-<scale_label>_atlas.nii.gz``
- ``anat/sub-<subject_label>_atlas-<atlas_label>[_res-<scale_label>]_dseg.nii.gz``

where:

where ``<scale_label>`` : ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5`` corresponds to the parcellation scale.
- ``<atlas_label>``:``Desikan``/``L2008``/``L2018``
is the parcellation scheme used
- ``<scale_label>``: ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5``
corresponds to the parcellation scale if applicable

with the description of parcel labels and the updated FreeSurfer color lookup table:

- ``anat/sub-<subject_label>_label-L2018_desc-<scale_label>_atlas.graphml``
- ``anat/sub-<subject_label>_label-L2018_desc-<scale_label>_atlas_FreeSurferColorLUT.txt``
- ``anat/sub-<subject_label>_atlas-<atlas_label>[_res-<scale_label>]_dseg.graphml``
- ``anat/sub-<subject_label>_atlas_atlas-<atlas_label>[_res-<scale_label>]_FreeSurferColorLUT.txt``

* Anatomical derivatives in the``DWI`` space produced by the diffusion pipeline are placed in each subject's ``anat/`` subfolder, including:

Expand All @@ -80,18 +91,21 @@ Anatomical derivatives

* The five different brain parcellation are saved as:

- ``anat/sub-<subject_label>_space-DWI_label-<atlas_label>_desc-<scale_label>_atlas.nii.gz``
- ``anat/sub-<subject_label>_space-DWI_atlas-<atlas_label>[_res-<scale_label>]_dseg.nii.gz``

where:
where:

- ``<atlas_label>``:``Desikan``/``L2008``/``L2018`` is the parcellation scheme used
- ``<scale_label>`` : ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5`` corresponds to the parcellation scale.
- ``<atlas_label>``:``Desikan``/``L2008``/``L2018``
is the parcellation scheme used
- ``<scale_label>``: ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5``
corresponds to the parcellation scale if applicable

* The 5TT image used for Anatomically Constrained Tractorgaphy (ACT):

- ``anat/sub-<subject_label>_space-DWI_label-5TT_probseg.nii.gz``

* The patial volume maps for white matter (WM), gray matter (GM), and Cortical Spinal Fluid (CSF) used for Particale Filtering Tractography (PFT), generated from 5TT image:
* The patial volume maps for white matter (WM), gray matter (GM), and Cortical Spinal Fluid (CSF) used
for Particale Filtering Tractography (PFT), generated from 5TT image:

- ``anat/sub-<subject_label>_space-DWI_label-WM_probseg.nii.gz``
- ``anat/sub-<subject_label_space-DWI>_label-GM_probseg.nii.gz``
Expand All @@ -104,9 +118,11 @@ Anatomical derivatives

Diffusion derivatives
------------------------
Diffusion derivatives in the individual ``DWI`` space are placed in each subject's ``dwi/`` subfolder, including:
Diffusion derivatives in the individual ``DWI`` space are placed in
each subject's ``dwi/`` subfolder, including:

* The final preprocessed DWI image used to fit the diffusion model for tensor or fiber orientation distribution estimation:
* The final preprocessed DWI image used to fit the diffusion model
for tensor or fiber orientation distribution estimation:

- ``dwi/sub-<subject_label>_desc-preproc_dwi.nii.gz``

Expand All @@ -124,7 +140,8 @@ Diffusion derivatives in the individual ``DWI`` space are placed in each subject
- ``dwi/sub-<subject_label>]_model-DTI_MD.nii.gz``


* The Fiber Orientation Distribution (FOD) image from Constrained Spherical Deconvolution (CSD) fit (if performed):
* The Fiber Orientation Distribution (FOD) image from
Constrained Spherical Deconvolution (CSD) fit (if performed):

- ``dwi/sub-<subject_label>]_model-CSD_diffmodel.nii.gz``

Expand All @@ -133,7 +150,9 @@ Diffusion derivatives in the individual ``DWI`` space are placed in each subject

- ``dwi/sub-<subject_label>]_model-MAPMRI_diffmodel.nii.gz``

with derived Generalized Fractional Anisotropic (GFA), Mean Squared Displacement (MSD), Return-to-Origin Probability (RTOP) and Return-to-Plane Probability (RTPP) maps:
with derived Generalized Fractional Anisotropic (GFA),
Mean Squared Displacement (MSD), Return-to-Origin Probability (RTOP)
and Return-to-Plane Probability (RTPP) maps:

- ``dwi/sub-<subject_label>]_model-MAPMRI_GFA.nii.gz``
- ``dwi/sub-<subject_label>]_model-MAPMRI_MSD.nii.gz``
Expand All @@ -144,7 +163,8 @@ Diffusion derivatives in the individual ``DWI`` space are placed in each subject

- ``dwi/sub-<subject_label>]_model-SHORE_diffmodel.nii.gz``

with derived Generalized Fractional Anisotropic (GFA), Mean Squared Displacement (MSD), Return-to-Origin Probability (RTOP) maps:
with derived Generalized Fractional Anisotropic (GFA),
Mean Squared Displacement (MSD), Return-to-Origin Probability (RTOP) maps:

- ``dwi/sub-<subject_label>]_model-SHORE_GFA.nii.gz``
- ``dwi/sub-<subject_label>]_model-SHORE_MSD.nii.gz``
Expand All @@ -156,23 +176,29 @@ Diffusion derivatives in the individual ``DWI`` space are placed in each subject

where:

- ``<model_label>`` is the diffusion model used to drive tractography (DTI, CSD, SHORE)
- ``<label>`` is the type of tractography algorithm employed (DET for deterministic, PROB for probabilistic)
- ``<model_label>`` is the diffusion model used to drive tractography
(DTI, CSD, SHORE)
- ``<label>`` is the type of tractography algorithm employed
(DET for deterministic, PROB for probabilistic)

* The structural connectivity (SC) graphs:

- ``dwi/sub-<subject_label>__label-<atlas_label>(_desc-<scale_label>)_conndata-network_connectivity.<format>``
- ``dwi/sub-<subject_label>_atlas-<atlas_label>[_res-<scale_label>]_conndata-network_connectivity.<format>``

where:

- ``<atlas_label>``:``Desikan``/``L2008``/``L2018`` is the parcellation scheme used
- ``<scale_label>``: ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5`` corresponds to the parcellation scale if applicable
- ``<format>``: ``mat``/``gpickle``/``tsv``/``graphml`` is the prefered format employed to stored the graph.
- ``<atlas_label>``:``Desikan``/``L2008``/``L2018``
is the parcellation scheme used
- ``<scale_label>``: ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5``
corresponds to the parcellation scale if applicable
- ``<format>``: ``mat``/``gpickle``/``tsv``/``graphml`` is the preferred format
employed to stored the graph.


Functional derivatives
-------------------------------
Functional derivatives in the 'meanBOLD' (individual) space are placed in each subject's ``func/`` subfolder including:
Functional derivatives in the 'meanBOLD' (individual) space are placed in
each subject's ``func/`` subfolder including:

* The original BOLD image:

Expand Down Expand Up @@ -204,20 +230,24 @@ Functional derivatives in the 'meanBOLD' (individual) space are placed in each s

* The ROI time-series for each parcellation scale:

- ``func/sub-<subject_label>_atlas-L2018_desc-<scale_label>_timeseries.npy``
- ``func/sub-<subject_label>_atlas-L2018_desc-<scale_label>_timeseries.mat``
- ``func/sub-<subject_label>_atlas-<atlas_label>[_res-<scale_label>]_timeseries.npy``
- ``func/sub-<subject_label>_atlas-<atlas_label>[_res-<scale_label>]_timeseries.mat``

where ``<scale_label>`` : ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5`` corresponds to the parcellation scale
where ``<scale_label>`` : ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5``
corresponds to the parcellation scale if applicable

* The functional connectivity (FC) graphs:

- ``func/sub-<subject_label>__label-<atlas_label>(_desc-<scale_label>)_conndata-network_connectivity.<format>``
- ``func/sub-<subject_label>_atlas-<atlas_label>[_res-<scale_label>]_conndata-network_connectivity.<format>``

where:

- ``<atlas_label>``:``Desikan``, ``L2008``, ``L2018`` is the parcellation scheme used
- ``<scale_label>``: ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5`` corresponds to the parcellation scale if applicable
- ``<format>``: ``mat``, ``gpickle``, ``tsv``, ``graphml`` is the prefered format employed to stored the graph
- ``<atlas_label>``:``Desikan``/``L2008``/``L2018``
is the parcellation scheme used
- ``<scale_label>``: ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5``
corresponds to the parcellation scale if applicable
- ``<format>``: ``mat``, ``gpickle``, ``tsv``, ``graphml`` is
the preferred format employed to stored the graph


FreeSurfer Derivatives
Expand Down

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