<commit_before>.. include:: links.rst

ds005
=====

``fmriprep``'s ds005 pipeline is used on datasets for which there are only t1ws and at least one functional (EPI) file.
Use the `--workflow-type ds005` or allow ``fmriprep`` to automatically determine the approriate workflow.

What It Does
------------
High-level view of the ds005 pipeline:

.. image:: ds005.dot.png

BIDSDatasource
~~~~~~~~~~~~~~

This node reads the BIDS_-formatted t1 data.

t1w_preprocessing
~~~~~~~~~~~~~~~~~

.. image:: t1w_preprocessing.dot.png

The t1w_preprocessing sub-workflow finds the skull stripping mask and the white matter/gray matter/cerebrospinal fluid segments.

EPI_HMC
~~~~~~~

.. image:: EPI_HMC.dot.png

The EPI_HMC sub-workflow collects BIDS_-formatted EPI files and performs head motion correction.

EPIMeanNormalization
~~~~~~~~~~~~~~~~~~~~

.. image:: EPIMeanNormalization.dot.png

The EPIMeanNormalization sub-workflow uses FSL FLIRT with the BBR cost function to find the transform that maps the EPI space into the T1-space.

EPIMNITransformation
~~~~~~~~~~~~~~~~~~~~

.. image:: EPIMNITransformation.dot.png

The EPIMNITransformation sub-workflow uses the transform from `EPIMeanNormalization`_ and a t1-to-MNI transform from `t1w_preprocessing`_ to map the EPI image to standardized MNI space.
It also maps the t1w-based mask to MNI space.

Transforms are concatenated and applied all at once, with one interpolation step, so as little information is lost as possible.

ConfoundDiscoverer
~~~~~~~~~~~~~~~~~~

.. image:: ConfoundDiscoverer.dot.png

Given a motion-corrected fMRI, a brain mask, MCFLIRT movement parameters and a segmentation, the ConfoundDiscoverer sub-workflow calculates potential confounds per volume.
Calculated confounds include the mean global signal, mean tissue class signal, tCompCor, aCompCor, and DVARS.


Reports
-------

``fmriprep`` outputs summary reports and reportlets (reports of individual steps in the process).
These reports provide visuals to make visual inspection of the results easy.

:download:`View a sample report. <_static/sample_report.html>`

Derivatives
-----------
<commit_msg>make graphs clickable<commit_after>.. include:: links.rst

ds005
=====

``fmriprep``'s ds005 pipeline is used on datasets for which there are only t1ws and at least one functional (EPI) file.
Use the `--workflow-type ds005` or allow ``fmriprep`` to automatically determine the approriate workflow.

What It Does
------------
High-level view of the ds005 pipeline:

.. image:: ds005.dot.png
    :scale: 100%

BIDSDatasource
~~~~~~~~~~~~~~

This node reads the BIDS_-formatted t1 data.

t1w_preprocessing
~~~~~~~~~~~~~~~~~

.. image:: t1w_preprocessing.dot.png
    :scale: 100%

The t1w_preprocessing sub-workflow finds the skull stripping mask and the white matter/gray matter/cerebrospinal fluid segments.

EPI_HMC
~~~~~~~

.. image:: EPI_HMC.dot.png
    :scale: 100%

The EPI_HMC sub-workflow collects BIDS_-formatted EPI files and performs head motion correction.

EPIMeanNormalization
~~~~~~~~~~~~~~~~~~~~

.. image:: EPIMeanNormalization.dot.png
    :scale: 100%

The EPIMeanNormalization sub-workflow uses FSL FLIRT with the BBR cost function to find the transform that maps the EPI space into the T1-space.

EPIMNITransformation
~~~~~~~~~~~~~~~~~~~~

.. image:: EPIMNITransformation.dot.png
    :scale: 100%

The EPIMNITransformation sub-workflow uses the transform from `EPIMeanNormalization`_ and a t1-to-MNI transform from `t1w_preprocessing`_ to map the EPI image to standardized MNI space.
It also maps the t1w-based mask to MNI space.

Transforms are concatenated and applied all at once, with one interpolation step, so as little information is lost as possible.

ConfoundDiscoverer
~~~~~~~~~~~~~~~~~~

.. image:: ConfoundDiscoverer.dot.png
    :scale: 100%

Given a motion-corrected fMRI, a brain mask, MCFLIRT movement parameters and a segmentation, the ConfoundDiscoverer sub-workflow calculates potential confounds per volume.
Calculated confounds include the mean global signal, mean tissue class signal, tCompCor, aCompCor, and DVARS.


Reports
-------

``fmriprep`` outputs summary reports and reportlets (reports of individual steps in the process).
These reports provide visuals to make visual inspection of the results easy.

:download:`View a sample report. <_static/sample_report.html>`

Derivatives
-----------

{'fraction_non_alphanumeric': 0.11778185151237397, 'fraction_numerical': 0.015123739688359304, 'mean_word_length': 4.532319391634981, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2075480', 'n_tokens_mistral': 1368, 'n_tokens_neox': 1249, 'n_words': 496}