:topic: CoNNECT Broad Analysis Tools

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CoNNECT Broad Analysis Tools
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There are many custom analysis tools that have been developed to provide broad processing capabilities across projects, MRI scanners, imaging parameters, and processing 
specifications. These tools are described in this Section. Many of these tools utilize a common JSON architecture to describe project-specific inputs that are utilized 
by these analysis tools to allow maximum flexibility of their implementation. Specifics to these JSON control files can be found at :ref:`project-specific_JSON_control_files`. 

.. note:: At this time, these functions only support command-line usage. 

.. include:: connect_create_project_db.rst

.. include:: connect_create_raw_nii.rst

.. include:: connect_dcm2nii.rst

.. include:: connect_flirt.rst

..
    .. include:: connect_mri_system_log_grabber.rst

.. include:: connect_neuro_db_query.rst

.. include:: connect_neuro_db_update.rst

.. include:: connect_pacs_dicom_grabber.rst

.. include:: connect_rawdata_check.rst

..
    .. include:: connect_sourcedata_check.rst