Sep 01, 2025

Public workspaceDATA STRUCTURE AND QUALITY CONTROL NEUROCHEMISTRY_H PIPELINE (CONNExIN 2025) V.1

DOI
https://dx.doi.org/10.17504/protocols.io.8epv5krpjv1b/v1
  • Ethan Draper1,
  • Hande Halilibrahimoğlu2,
  • Abdallah Z Mohamed3,
  • kesavi Kanagasabai4,
  • Akinkunmi Phoebe5,
  • Fuhad Bankole6,
  • ajiscomorac 7,
  • godswillchidubem 8,
  • Ahmad Abdullahi9
  • 1Montreal Neurological Institute, McGill University, Montreal, Canada & Oxford University Centre for Integrative Neuroimaging, Oxford University;
  • 2Montreal Neurological Institute, McGill University, Montreal, Canada;
  • 3United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates;
  • 4Western University, London, Ontario, Canada;
  • 5Physics with Electronics, Bells University of Technology Nigeria;
  • 6University of greater Manchester, MSc biomedical engineering;
  • 7AI Engineering and Research, HelpMum;
  • 8Medical student, Nigeria;
  • 9Yobe State University Teaching Hospital, Damaturu
akinkunmi phoebe
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DOI: https://dx.doi.org/10.17504/protocols.io.8epv5krpjv1b/v1
Protocol Citation: Ethan Draper, Hande Halilibrahimoğlu, Abdallah Z Mohamed, kesavi Kanagasabai, Akinkunmi Phoebe, Fuhad Bankole, ajiscomorac , godswillchidubem , Ahmad Abdullahi 2025. DATA STRUCTURE AND QUALITY CONTROL NEUROCHEMISTRY_H PIPELINE (CONNExIN 2025). protocols.io https://dx.doi.org/10.17504/protocols.io.8epv5krpjv1b/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: August 27, 2025
Last Modified: September 01, 2025
Protocol Integer ID: 225653
Keywords: MRI preprocessing, Dementia, MRIQC, quality control neurochemistry-h pipeline, connexin
Abstract
CONNExIN 2025 Neurochemistry H team analysis pipeline
Troubleshooting
DATA STRUCTURE
Define project directories:
$BIDS_DIR- root of BIDS dataset (e.g., "~/bids_dataset")
$RAW_DICOM_DIR- source DICOMs (e.g., "~/raw_dicom/sub-064/ses-03/func")
Create subject/session folders
sub-064/ses-03/func
Convert DICOM to NlfTI:
NIfTI + JSON (keep BIDS names)
Validate BIDS Structure
bids-validator /neurodesktop-storage/bids/
QUALITY CONTROL
Motion assessment:
Calculate frame wise displacement using FSL (e.g. mcflirt -in "$FMRI" -out motion_corrected -plots -rmsrel -rmsabs)
QUALITY CONTROL
Generate motion plots:
Create motion parameter visualization (e.g. fsl_motion_outliers -i "$FMRI" -o motion_outliers.txt --fd --thresh=0.2 -p motion_plot)
Signal-To-Noise-Ratio:
Calculate temporal SNR using AFNI (available in NeuroDesktop) (e.g. 3dTstat -cvarinv -prefix tSNR "$FMRI")