.. _conversion:

Conversion
==========

.. _download:

Download
--------

#. Download the appropriate files from UT Southwestern's AIRC website (`https://swlxaircweb.swmed.edu/ <https://swlxaircweb.swmed.edu/>`_) to ``/raid/data/shared/incoming/airc/``
   
   Make the zip file name completely lowercase and should match the following:
   ``<airc_id>_<sub>_w<1|2|3>/``
   
   However, if there is no study ID such as the participant being a pilot, it can be:
   ``<airc_id>/`` or ``<airc_id>_w<1|2|3>/``


.. _convert:

Convert
-------

.. note::

   Install the following package if you have not run this before:

   .. code:: bash

      module load python/3.8.6
      pip install --user git+https://github.com/epongpipat/pyHelperKennedyRodrigue.git


#. Load appropriate modules and set parameters for subsequent code

   .. code:: bash

      module load sge
      module load python/3.8.6
      root_dir='/raid/data'
      airc_id=""
      sub=""
      ses=""

#. Convert MRI

   .. code:: bash

      code_dir="${root_dir}/shared/software/scripts/eep170030/mri/convert"
      bash ${code_dir}/convert_uber.sh \
      --airc_id ${airc_id} \
      --sub ${sub} \
      --ses ${ses}

   The code performs the following:
   
   1. unzip files and rename the output directory to lowercase
   2. sort the DICOM files into their appropriate directories by series name
   3. convert files from DICOM to NIfTI using dcm2niix

   After the script is done, check the conversion and move bad files (e.g., incomplete acquisitions) into a ``bad/`` directory

.. _qc:

QC Parameters
-------------

#. Create QC files

   .. code:: bash

      code_dir="${root_dir}/shared/software/scripts/eep170030/mri/qc_mri"
      bash ${code_dir}/qc_uber.sh \
      --airc_id ${airc_id} \
      --sub ${sub}

   The code performs the following:

   1. converts dcm2niix bids output from .json to .csv format
   2. combines dcm2niix bids output (.csv) across participants by acquisition
   3. converts fslhd output to .csv format
   4. combines fslhd output (.csv) across participants by acquisition
   5. combines all .csv output by acquisition

#.  Create QC report

   .. note::

      The following code needs to be run locally. The server does not currently have a compatible pandoc version

   .. code:: bash

      code_dir="${root_dir}/shared/software/scripts/eep170030/mri/qc_mri/rmd"
      Rscript ${code_dir}/render-rmds.R


   Six (6) QC html reports will be updated/saved in ``${root_dir}/shared/incoming/qc/derivatives/sub-differences/rmd-html``. Please review and any potential outliers in either qualitative or quantitive values, and bring up any potential concerns to the team.

.. _copy:

Copy Files
----------

#. Copy and rename files

   .. note:: 

      may need to install the following if running for the first time:

      .. code:: bash

         Rscript -e 'devtools::install_github("epongpipat/rHelperKennedyRodrigue")'

   .. code:: bash

      code_dir="${root_dir}/shared/software/scripts/eep170030/mri/modality_specific_conversion"
      bash ${code_dir}/modality_specific_conversion/copy_files_uber.sh \
      --airc_id ${airc_id} \
      --sub ${sub}

   The code performs the following:

   1. copy files into an ``original/`` directory
   2. rename and merge/split files volumes to match prior convention