Add basic derivatives/pybids content

Author: effigies

docs/assets/fmriprep-bootcamp-geneva2024/day1-02-bids/index.html

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+      .install-cmd {
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 ]
 
 ---
+template: newsection
+layout: true
+name: Derivatives
+
+# BIDS Derivatives
+
+---
+
+BIDS Derivatives generally mirror the raw dataset.
+
+.small[
+.pad-left[
+<i class="fa-solid fa-folder-open"></i> fmriprep/<br />
+.pad-left[<i class="fa-solid fa-file-lines"></i> README]<br />
+.pad-left[<i class="fa-solid fa-circle-info"></i> dataset_description.json]<br />
+.pad-left[<i class="fa-solid fa-folder-open"></i> sub-11]<br />
+.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> anat/]]<br />
+.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_desc-preproc_T2w.nii.gz]]]<br />
+.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_acq-denoised_desc-preproc_T1w.nii.gz]]]<br />
+.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_acq-denoised_desc-brain_mask.nii.gz]]]<br />
+.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_acq-denoised_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5]]]<br />
+.pad-left[.pad-left[.pad-left[<i class="fa-blank fa-brain"></i> ...]]]<br />
+.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> fmap/]]<br />
+.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_fmapid-auto00000_desc-coeff_fieldmap.nii.gz]]]<br />
+.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz]]]<br />
+.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_fmapid-auto00000_desc-preproc_fieldmap.nii.gz]]]<br />
+.pad-left[.pad-left[<i class="fa-solid fa-folder-open"></i> func/]]<br />
+.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_task-mixed_desc-coreg_boldref.nii.gz]]]<br />
+.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_task-mixed_desc-hmc_boldref.nii.gz]]]<br />
+.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-file-lines"></i> sub-11_task-mixed_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt]]]<br />
+.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-file-lines"></i> sub-11_task-mixed_from-boldref_to-auto00000_mode-image_desc-fmapreg_xfm.txt]]]<br />
+.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_task-mixed_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt]]]<br />
+.pad-left[.pad-left[.pad-left[<i class="fa-solid fa-brain"></i> sub-11_task-mixed_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz]]]<br />
+.pad-left[.pad-left[.pad-left[<i class="fa-blank fa-brain"></i> ...]]]<br />
+.pad-left[<i class="fa-solid fa-folder"></i> sub-14]<br />
+.pad-left[<i class="fa-solid fa-folder"></i> sub-15]<br />
+]
+]
+
+--
+
+New file suffixes, extensions and entities are possible.
+
+---
+template: newsection
+layout: true
+name: PyBIDS
+
+.install-cmd[
+```Bash
+pip install pybids
+```
+]
+
+---
+
+# PyBIDS
+
+A common specification of neuroimaging datasets affords queries for and
+adaptation to the available data.
+
+[PyBIDS](https://github.com/bids-standard/pybids/) is a Python library for
+querying and manipulating BIDS datasets.
+
+
+```Python
+>>> from bids import BIDSLayout
+>>> layout = BIDSLayout('/my_dataset')
+>>> bold = layout.get(subject='11', task='rest', suffix='bold', extension='.nii.gz')
+>>> bold
+[<BIDSImageFile filename='/my_dataset/sub-11/func/sub-11_task-rest_bold.nii.gz'>]
+>>> md = bold[0].get_metadata()
+>>> md['RepetitionTime']
+1.5
+>>> bold[0].get_entities()
+{'datatype': 'func',
+ 'extension': '.nii.gz',
+ 'subject': '11',
+ 'suffix': 'bold',
+ 'task': 'rest'}
+```
+
+---
+
+# PyBIDS - Derivatives
+
+PyBIDS layouts support BIDS derivatives:
+
+```Python
+>>> fmri_derivs = BIDSLayout('/my_dataset-fmriprep', config=['bids', 'derivatives'], validate=False)
+>>> spaces = fmri_derivs.get_spaces(desc='preproc', suffix='bold')
+>>> spaces
+['MNI152NLin2009cAsym']
+```
+
+--
+
+It is also possible to provide your own config:
+
+```Python
+>>> import niworkflows
+>>> nipreps_config = niworkflows.data.load('nipreps.json')
+>>> fmri_derivs = BIDSLayout('/my_dataset-fmriprep, config=[nipreps_config], validate=False)
+```
+
+---
+template: newsection
 
-## Conclusion
+# Conclusion
 
 .boxed-content[
 .distribute.large[