fMRIPrep Bootcamp | Day 1 :: Brain Imaging Data Structure

name: title
layout: true
class: center
---
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.center[
<a href="https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/day1-02-bids/">
 <img src="images/qr-talk-url.svg" alt="workflow" style="width: 20%" />
 
 https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/day1-02-bids/
</a>

## The Brain Imaging Data Structure (BIDS)

Chris Markiewicz <<code>markiewicz@stanford.edu</code>>

Oscar Esteban <<code>phd@oscaresteban.es</code>>

]

???

NOTES TO OURSELVES GO HERE

---
name: newsection
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.perma-sidebar[

<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0; height: 20px; padding-top: 6px;" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a>
 Day 1 :: Brain Imaging Data Structure

]

---

.boxed-content[
.large.center[
.larger.center.gray-text[Before we start...]
## What do you think/know about BIDS?
]]

---
layout: true
template: newsection
name: BIDS

# BIDS: Brain Imaging Data Structure

.left-column2.small[
.pad-left[
 my_dataset/ 
.pad-left[ CHANGES] 
.pad-left[ README] 
.pad-left[ dataset_description.json] 
.pad-left[ participants.json] 
.pad-left[ participants.tsv] 
.pad-left[ scans.json] 
.pad-left[ sub-11] 
.pad-left[.pad-left[ anat/]] 
.pad-left[.pad-left[.pad-left[ sub-11_T2w.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_T2w.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_acq-denoised_T1w.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_acq-denoised_T1w.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_acq-mp2rage_T1w.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_acq-mp2rage_T1w.nii.gz]]] 
.pad-left[.pad-left[ fmap/]] 
.pad-left[.pad-left[.pad-left[ sub-11_magnitude1.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_magnitude1.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_magnitude2.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_magnitude2.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_phasediff.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_phasediff.nii.gz]]] 
.pad-left[.pad-left[ func/]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-mixed_bold.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-mixed_bold.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-mixed_events.tsv]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-rest_bold.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-rest_bold.nii.gz]]] 
.pad-left[.pad-left[ sub-11_scans.tsv]] 
.pad-left[ sub-14] 
.pad-left[ sub-15] 
]
]

---

.right-column2.larger[

* BIDS is a directory structure, based on common practices

* Builds on existing standards (NIfTI, JSON, TSV)

* Intended for human *and* machine legibility

* The [BIDS Validator](https://bids-standard.github.io/bids-validator)
  makes compliance easy to verify

* The [specification](https://bids-specification.readthedocs.io/en/stable/)
  is a searchable HTML document
]

---

.right-column2[.no-bullet[* .larger[Basic metadata in the file names]
  * Subject, session, imaging modality, etc.
  * Generally just enough to assign unique names]]
--
.right-column2[.no-bullet[* .larger[NIfTI headers and *JSON sidecars* contain detailed,
  image-related metadata]]]
--
.right-column2[.no-bullet[* .larger[Study-level metadata]
  * Not necessarily associated with specific files
  * [`dataset_description.json`](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#dataset_descriptionjson),
    [`participants.tsv`](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#participants-file),
    [`sessions.tsv`](https://bids-specification.readthedocs.io/en/stable/05-longitudinal-and-multi-site-studies.html#sessions-file),
    and [`scans.tsv`](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#scans-file)
]]

---
template: newsection
layout: true

---
 
.boxed-content[
<figure style="width: 100%">
![:img timeline, 100%](images/timeline.png)
</figure>
]

---

# A staggering pace of adoption

.boxed-content[
<figure style="width: 100%">
![:img timeline, 100%](images/bids-growth.png)
</figure>
]

---

# bids-specification.readthedocs.io

.boxed-content[
<iframe src="https://bids-specification.readthedocs.io/en/stable/" width="100%" height="540px" style="border: 0; margin-top: 15px" />
]

---

# More reproducible research

.boxed-content[
.no-bullet[
* .larger[ BIDS defines a clear interface]
 * Standardized through a large-community agreement
 * Human readable (as opposed to DICOM)
 * Machine readable (enabling tooling, see below)
 * Stable (e.g., backward compatibility principle), extensible, and predictable (*BIDS Schema*)

* .larger[ Harnesses data-sharing and archival (sharing with self)]
 * Can be checked for correctness (*BIDS Validator*)
 * Establishes a solid *contract* on the organization of data between authors and reusers (or your future self)
 * Separates *data blobs* and metadata, facilitating agile management and understanding of the dataset, HPC operations (e.g., *datalad drop*), etc.
 * Enables open-sharing (e.g., *OpenNeuro*)

* .larger[ Supports tooling]
 * Querying the dataset, filtering data, etc. (*PyBIDS*)
 * Conversion from other formats (mostly *DICOM*)
 * Interpreting unprocessed data (development of *BIDS Apps* such as *MRIQC* or *fMRIPrep*)
 * *BIDS Derivatives* enable concatenating *BIDS Apps* (e.g., *fMRIPrep* + *XCPD*, *brainlife.io*)
 * Data-management-friendly (*DataLad*)
]
]

---

# BIDS Validator

.boxed-content[
The machine-readable structure makes validation possible:

``` bash
$ bids-validator my_dataset/
bids-validator@1.14.6

1: [WARN] The recommended file /README is very small. Please consider expanding it with additional information about the dataset. (code: 213 - README_FILE_SMALL)
    ./README

Please visit https://neurostars.org/search?q=README_FILE_SMALL for existing conversations about this issue.

Summary:                Available Tasks:                            Available Modalities: 
        96 Files, 6.63GB        Mixed-stimuli, positive-control task        MRI                   
        5 - Subjects            Resting-state fMRI                                                
        1 - Session

If you have any questions, please post on https://neurostars.org/tags/bids.
```

.center[
## https://bids-standard.github.io/bids-validator/
]]

---

# BIDS Validator

.boxed-content[
Once all warnings and errors are addressed:

``` bash
$ bids-validator my_dataset/
bids-validator@1.14.6

This dataset appears to be BIDS compatible.
        Summary:                Available Tasks:                            Available Modalities: 
        96 Files, 6.63GB        Mixed-stimuli, positive-control task        MRI                   
        5 - Subjects            Resting-state fMRI                                                
        1 - Session

If you have any questions, please post on https://neurostars.org/tags/bids.
```

.center[
## https://bids-standard.github.io/bids-validator/
]]

---

# Sharing through OpenNeuro

.boxed-content[
.center[[https://openneuro.org/datasets/ds005454/versions/1.0.0](https://openneuro.org/datasets/ds005454/versions/1.0.0)]

---
layout: true
template: newsection
name: Apps

# BIDS Applications

---
A common specification of neuroimaging datasets affords queries for and
adaptation to the available data.
--
.boxed-content[
Queryable (meta)data allows a very simple protocol for a
[BIDS App](https://bids-apps.neuroimaging.io/apps/):

```Bash
bids-app /bids-directory /output-directory participant [OPTIONS]
```

.footnote[
\* Note that `participant` is an analysis level. Apps may also operate
at the `run`, `session` or `group` levels.
]]

.boxed-content[
## Examples

**MRIQC**

```Bash
mriqc /data/bids/openneuro/ds000228 /data/processed/ds000228-mriqc group
```
]
--

.boxed-content[
**fMRIPrep**

```Bash
fmriprep /data/bids/openneuro/ds000228 /data/processed/ds000228-fmriprep \
    participant --participant-label pixar001
```
]
---

.pull-left[
### Many application types are possible
]
.pull-right[
[![:img BIDS App list, 75%](images/bids-apps.png)](https://bids-apps.neuroimaging.io/apps/)
]

---
count: false

.pull-left[
### Many application types are possible

* Quality control

]
.pull-right[
[![:img BIDS QC Apps, 75%](images/bids-apps-qc.png)](https://bids-apps.neuroimaging.io/apps/)
]

---
count: false

.pull-left[
### Many application types are possible

* Quality control

* Anatomical pipelines

]
.pull-right[
[![:img BIDS Anatomical Apps, 75%](images/bids-apps-anatomical.png)](https://bids-apps.neuroimaging.io/apps/)
]

---
count: false

.pull-left[
### Many application types are possible

* Quality control

* Anatomical pipelines

* Functional pipelines

]
.pull-right[
[![:img BIDS Functional Apps, 75%](images/bids-apps-functional.png)](https://bids-apps.neuroimaging.io/apps/)
]

---
count: false

.pull-left[
### Many application types are possible

* Quality control

* Anatomical pipelines

* Functional pipelines

* Diffusion pipelines

]
.pull-right[
[![:img BIDS Diffusion Apps, 75%](images/bids-apps-diffusion.png)](https://bids-apps.neuroimaging.io/apps/)
]

---
count: false

.pull-left[
### Many application types are possible

* Quality control

* Anatomical pipelines

* Functional pipelines

* Diffusion pipelines

### Lowered friction encourages adoption

* Researchers gain easy access to tools by formatting data
  in BIDS

* Accepting BIDS datasets makes your tools easy to try

]
.pull-right[
[![:img BIDS App list, 75%](images/bids-apps.png)](https://bids-apps.neuroimaging.io/apps/)
]

---
template: newsection
layout: true
name: Derivatives

# BIDS Derivatives

---

BIDS Derivatives generally mirror the raw dataset.

.small[
.pad-left[
 fmriprep/ 
.pad-left[ README] 
.pad-left[ dataset_description.json] 
.pad-left[ sub-11] 
.pad-left[.pad-left[ anat/]] 
.pad-left[.pad-left[.pad-left[ sub-11_desc-preproc_T2w.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_acq-denoised_desc-preproc_T1w.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_acq-denoised_desc-brain_mask.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_acq-denoised_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5]]] 
.pad-left[.pad-left[.pad-left[ ...]]] 
.pad-left[.pad-left[ fmap/]] 
.pad-left[.pad-left[.pad-left[ sub-11_fmapid-auto00000_desc-coeff_fieldmap.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_fmapid-auto00000_desc-preproc_fieldmap.nii.gz]]] 
.pad-left[.pad-left[ func/]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-mixed_desc-coreg_boldref.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-mixed_desc-hmc_boldref.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-mixed_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-mixed_from-boldref_to-auto00000_mode-image_desc-fmapreg_xfm.txt]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-mixed_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-mixed_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ ...]]] 
.pad-left[ sub-14] 
.pad-left[ sub-15] 
]
]

New file suffixes, extensions and entities are possible.

---
template: newsection
layout: true
name: PyBIDS

.install-cmd[
```Bash
pip install pybids
```
]

---

# PyBIDS

.boxed-content[
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

.boxed-content[
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']
```
]
--

.boxed-content[
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)
```
]
---

# PyBIDS | Large datasets

.boxed-content[
 
.larger[*BIDS Apps* can spend long time indexing if they rely on *PyBIDS* ]
.no-bullet[
* **create a cache**:
]

```Bash
$ pybids layout --reset-db --no-validate --index-metadata . /my_dataset/.bids-index/
```

.larger[And then inform your *BIDS App*.]

In the case of *MRIQC* and *fMRIPrep*, point the `--bids-database-dir` argument to the newly created cache:

```Bash
$ mriqc /data/input /derivatives/output participant [OPTIONS] \
    --bids-database-dir /my_dataset/.bids-index/
```

```Bash
$ fmriprep /data/input /derivatives/output participant [OPTIONS] \
    --bids-database-dir /my_dataset/.bids-index/
```

]

---
template: newsection
layout: true
name: conversion
---

# Converting from DICOM into BIDS

.left-column-mid.small[
.pad-left[
 my_dataset/ 
.pad-left[ sub-11] 
.pad-left[.pad-left[ 10 - anat-T1w_acq-mp2rage_run-01_UNI_Images.dicom]] 
.pad-left[.pad-left[ 11 - anat-T1w_acq-mp2rage_run-01_UNI-DEN.dicom]] 
.pad-left[.pad-left[ 12 - anat-T1w_acq-mp2rage_run-01_INV2.dicom]] 
.pad-left[.pad-left[ 16 - fmap-gre_acq-siemens_run-01/]] 
.pad-left[.pad-left[.pad-left[ 1.3.12.2.1107.5.2.61.237203.20[...]25.MR.dcm]]] 
.pad-left[.pad-left[.pad-left[ 1.3.12.2.1107.5.2.61.237203.20[..]33.MR.dcm]]] 
.pad-left[.pad-left[ 17 - fmap-gre_acq-siemens_run-01.dicom ]] 
.pad-left[.pad-left[ 18 - func-bold_acq-midRes_task-rest_run-01/ ]] 
.pad-left[.pad-left[.pad-left[ 1.3.12.2.1107.5.2.61.237203.20[...]25.MR.dcm]]] 
.pad-left[.pad-left[.pad-left[]]] 
.pad-left[.pad-left[.pad-left[ 1.3.12.2.1107.5.2.61.237203.20[..]33.MR.dcm]]] 
.pad-left[.pad-left[ 20 - func-bold_acq-midRes_task-mixed_run-01/ ]] 
.pad-left[.pad-left[.pad-left[ 1.3.12.2.1107.5.2.61.237203.20[...]25.MR.dcm]]] 
.pad-left[.pad-left[.pad-left[]]] 
.pad-left[.pad-left[.pad-left[ 1.3.12.2.1107.5.2.61.237203.20[..]33.MR.dcm]]] 
.pad-left[.pad-left[ 22 - anat-T2w_acq-p6_run-01.dicom]] 
.pad-left[.pad-left[ 7 - anat-T1w_acq-mp2rage_run-01_INV1.dicom]] 
.pad-left[.pad-left[ 8 - anat-T1w_acq-mp2rage_run-01_T1_Images.dicom]] 
.pad-left[.pad-left[ 9 - anat-T1w_acq-mp2rage_run-01_T1_Images.dicom]] 
.pad-left[ sub-14] 
.pad-left[ sub-15] 
]
]

.right-column-mid[
.no-bullet[
* .larger[DICOM (Digital Imaging and Communications in Medicine)]
   * was originally meant for storage and transmission within/between machines.
* .larger[DICOM structures store their relevant metadata internally,]
   * but structure and fields tend to be vendor- & institution-specific.

* .larger[Constructing a BIDS dataset can be tedious and error-prone, so there are several
[converters](https://bids.neuroimaging.io/benefits.html#converters).] 
   * The [Heuristic DICOM Converter](https://heudiconv.readthedocs.io/) (HeuDiConv) and
[BIDSCoin](https://bidscoin.readthedocs.io/en/stable/) allow you to specify the mapping and
apply in bulk. Both build off of [dcm2niix](https://github.com/rordenlab/dcm2niix/).
]
]

---

# Converting from DICOM into BIDS

.right-column-mid.small[
.pad-left[
 my_dataset/ 
.pad-left[ CHANGES] 
.pad-left[ README] 
.pad-left[ dataset_description.json] 
.pad-left[ participants.json] 
.pad-left[ participants.tsv] 
.pad-left[ scans.json] 
.pad-left[ sub-11] 
.pad-left[.pad-left[ anat/]] 
.pad-left[.pad-left[.pad-left[ sub-11_T2w.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_T2w.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_acq-denoised_T1w.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_acq-denoised_T1w.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_acq-mp2rage_T1w.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_acq-mp2rage_T1w.nii.gz]]] 
.pad-left[.pad-left[ fmap/]] 
.pad-left[.pad-left[.pad-left[ sub-11_magnitude1.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_magnitude1.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_magnitude2.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_magnitude2.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_phasediff.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_phasediff.nii.gz]]] 
.pad-left[.pad-left[ func/]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-mixed_bold.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-mixed_bold.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-mixed_events.tsv]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-rest_bold.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-rest_bold.nii.gz]]] 
.pad-left[.pad-left[ sub-11_scans.tsv]] 
.pad-left[ sub-14] 
.pad-left[ sub-15] 
]
]

---

# DICOM-to-BIDS: ReproIn

.center[[ReproIn](https://github.com/ReproNim/reproin) standardizes protocol naming conventions:]

<figure style="width: 60%">
![:img HCPh-sops-naming, 100%](https://www.axonlab.org/hcph-sops/assets/images/launch_sequence.jpg)
<figcaption>From <a href="https://www.axonlab.org/hcph-sops">the HCPh SOPs</a>;
doi:![:doi](10.6084/m9.figshare.19579873.v1)</figcaption>
</figure>

---

<figure style="width: 60%">
![:img ReproIn conversion schema, 100%](images/dbic-conversions_cropped.png)
<figcaption>From <a href="https://github.com/ReproNim/reproin/blob/master/README.md#overall-workflow">ReproIn</a>;
doi:![:doi](10.5281/zenodo.1207117)</figcaption>

???

Please note that this figure is OUT OF DATE. For example, the anatomicals are called anat-T1W__, anat-T2w__ etc.

---

# DICOM-to-BIDS: HeuDiConv

.boxed-content.no-bullet[

* .large[ **Heu**ristic **DI**COM** Conv**erter: maps DICOM metadata into BIDS]

* .large[ Mappings are encoded within the *heuristic file*]

* The `.heudiconv/` folder contains the metadata that can be employed in the *heuristic file* to define mappings.

<figure style="width: 100%">
![:img HeuDiConv workflow, 100%](https://raw.githubusercontent.com/nipy/heudiconv/master/figs/workflow.png)
<figcaption>From <a href="https://github.com/nipy/heudiconv?tab=readme-ov-file#howto-101">HeuDiConv</a>;
doi:![:doi](10.5281/zenodo.1012598)</figcaption>

]

---

# DICOM-to-BIDS: HeuDiConv

.boxed-content[

.no-bullet.large[
*   Generate a **heuristic file**

*   Edit the **heuristic file**
]

.small[
```Python
data = create_key('run-{item:03d}')

t1w = create_key('sub-{subject}/{session}/anat/sub-{subject}_{session}_T1w')

dwi = create_key('sub-{subject}/{session}/dwi/sub-{subject}_{session}_dir-AP_dwi')

# Save the RPE (reverse phase-encode) B0 image as a fieldmap (fmap).  It will be used to correct
# the distortion in the DWI
fmap_rev_phase =  create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_dir-PA_epi')

fmap_mag =  create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_magnitude')

fmap_phase = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_phasediff')

# Even if this is resting state, you still need a task key
func_rest = create_key('sub-{subject}/{session}/func/sub-{subject}_{session}_task-rest_run-01_bold')
func_rest_post = create_key('sub-{subject}/{session}/func/sub-{subject}_{session}_task-rest_run-02_bold')
```
]

.no-bullet.large[
*   Execute *HeuDiConv*
]

]

---

# DICOM-to-BIDS: ReproIn + HeuDiConv

.no-bullet.large[
*   Just run *HeuDiConv* directly! *Heuristic file* is pre-defined.

*   What if I **did not** follow *ReproIn* namings?
]

.boxed-content.small[

``` Python
# A dictionary containing fixes/remapping for sequence names per study.
# Keys are md5sum of study_description from DICOMs, in the form of PI-Experimenter^protocolname
# You can use `heudiconv -f reproin --command ls --files PATH
# to list the "study hash".
# Values are list of tuples in the form (regex_pattern, substitution).
# If the key is an empty string "", it would apply to any study.
protocols2fix: dict[str | re.Pattern[str], list[tuple[str, str]]] = {
 "": [ # <-- empty string means apply to whole study
 ("anat-T1w_acq-mp2rage_run-01", "anat-mp2rage"),
 ("_UNI_", "_acq-mp2rage__"),
 ("_UNI-DEN", "_acq-denoised__"),
 ("_INV", "_inv-"),
 ("_T1_", "_acq-T1map__"),
 ("fmap_acq-siemens", "fmap-phasediff"),
 ("fmap-gre_acq-siemens", "fmap-phasediff"),
 ("_acq-midRes", ""),
 ("_acq-p6", ""),
 ("_run-01", ""),
 ]
}
```

]

---

# DICOM-to-BIDS: ReproIn + HeuDiConv

.left-column-mid[
Our dataset's DICOM had some non-compliant names:
.small[
.pad-left[
 my_dataset/ 
.pad-left[ sub-11] 
.pad-left[.pad-left[ 10 - anat-T1w_acq-mp2rage_run-01_UNI_Images.dicom]] 
.pad-left[.pad-left[ 11 - anat-T1w_acq-mp2rage_run-01_UNI-DEN.dicom]] 
.pad-left[.pad-left[ 12 - anat-T1w_acq-mp2rage_run-01_INV2.dicom]] 
.pad-left[.pad-left[ 16 - fmap-gre_acq-siemens_run-01/]] 
.pad-left[.pad-left[.pad-left[ 1.3.12.2.1107.5.2.61.237203.20[...]25.MR.dcm]]] 
.pad-left[.pad-left[.pad-left[ 1.3.12.2.1107.5.2.61.237203.20[..]33.MR.dcm]]] 
.pad-left[.pad-left[ 17 - fmap-gre_acq-siemens_run-01.dicom ]] 
.pad-left[.pad-left[ 18 - func-bold_acq-midRes_task-rest_run-01/ ]] 
.pad-left[.pad-left[.pad-left[ 1.3.12.2.1107.5.2.61.237203.20[...]25.MR.dcm]]] 
.pad-left[.pad-left[.pad-left[]]] 
.pad-left[.pad-left[.pad-left[ 1.3.12.2.1107.5.2.61.237203.20[..]33.MR.dcm]]] 
.pad-left[.pad-left[ 20 - func-bold_acq-midRes_task-mixed_run-01/ ]] 
.pad-left[.pad-left[.pad-left[ 1.3.12.2.1107.5.2.61.237203.20[...]25.MR.dcm]]] 
.pad-left[.pad-left[.pad-left[]]] 
.pad-left[.pad-left[.pad-left[ 1.3.12.2.1107.5.2.61.237203.20[..]33.MR.dcm]]] 
.pad-left[.pad-left[ 22 - anat-T2w_acq-p6_run-01.dicom]] 
.pad-left[.pad-left[ 7 - anat-T1w_acq-mp2rage_run-01_INV1.dicom]] 
.pad-left[.pad-left[ 8 - anat-T1w_acq-mp2rage_run-01_T1_Images.dicom]] 
.pad-left[.pad-left[ 9 - anat-T1w_acq-mp2rage_run-01_T1_Images.dicom]] 
.pad-left[ sub-14] 
.pad-left[ sub-15] 
]
]]

---

# DICOM-to-BIDS: HeuDiConv may not be sufficient

.boxed-content[
.no-bullet[
* .large[ **'events'** files describing the experiment's timeline]
]

.pad-left[
 my_dataset/ 
.pad-left[ sub-11] 
.pad-left[.pad-left[ func/]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-mixed_bold.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-mixed_bold.nii.gz]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-mixed_events.tsv]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-rest_bold.json]]] 
.pad-left[.pad-left[.pad-left[ sub-11_task-rest_bold.nii.gz]]] 
]

.no-bullet[
* .large[ **'physio'** files (physiological recordings, eye-tracking, etc.)]

* .large[ **'stim'** files (stimuli-related such as movies, task cues, etc.)]

* .large[ supporting metadata (e.g., field maps, covariates, phenotype, etc.)]
]
]

---

# Conclusion

.boxed-content[
.distribute.large[

]
]

???

---
layout: false
count: false

.center[
<a href="https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/day1-02-bids/"><img src="images/qr-talk-url.svg" alt="workflow" style="width: 20%" /></a>

## Thanks

#### Chris Markiewicz <<code>markiewicz@stanford.edu</code>> & Oscar Esteban <<code>phd@oscaresteban.es</code>>

The Brain Imaging Data Structure (BIDS)

Funding: [SNSF 185872](https://data.snf.ch/grants/grant/185872), [RF1MH121867](https://reporter.nih.gov/project-details/10260312), [CZI EOSS5-000266](https://chanzuckerberg.com/eoss/proposals/nipreps-a-community-framework-for-reproducible-neuroimaging/)

]

???