Welcome to the WSU’s Center of Neuroimaging and Neuro-Evaluation of Cognitive Technologies

CoNNECT houses a 3.0-Tesla Philips Ingenia Cx MRI system with focused neuroimaging research applications. This documentation describes the Data Management and Analysis pipelines that have been developed to ensure minimal data loss, expedited data processing and rapid project development.

Fig. 1 The Philips Ingenia Cx installed in the Neuroscience Engineering Building on Wright State’s Dayton campus.

Note

This manual is under active initial development.

Table of Contents

• Administration
• MRI Scheduling
  • View MRI Availability
  • Schedule Appointment
• Systems Overview
  • Philips 3.0T Ingenia Cx
  • Data Management
  • CoNNECT Neuro-Processing Cluster (NPC)
• Neuro-Processing Cluster (NPC)
  • Open-Source Software
  • MySQL Database
• CoNNECT Broad Analysis Tools
  • connect_create_project_db.py
  • connect_create_raw_nii.py
  • connect_dcm2nii.py
  • connect_flirt.py
  • connect_neuro_db_query.py
  • connect_neuro_db_update.py
  • connect_pacs_dicom_grabber.py
  • connect_rawdata_check.py
• Example Processing Procedures
  • Project Startup
• CoNNECT Support Tools
  • bids_commands.py
  • convert_dicoms.py
  • create_fsl_condor_job.py
  • create_python_condor_job.py
  • flirt.py
  • flirt_pngappend.py
  • get_scan_id.py
  • get_spec_base.py
  • mysql_commands.py
  • read_credentials.py
• Project-Specific JSON Control Files
  • Brain Extraction JSON Control File
  • FLIRT JSON Control File
  • Scan Identification JSON Control File