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DICOM to NIFTI Conversion

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Carl Helmick edited this page Jun 16, 2021 · 4 revisions

DICOM to NIFTI Conversion Details:

(typically ~10 minutes per subject)

This step assumes the T1w, T2w, DTI DICOM data have been downloaded to the shared drive from Horos, and RS Pfiles have been downloaded, organized, and already converted into NIFTI files with mux2nii.

The following steps convert the DICOMS data in the rawdata folder into NIFTI format.

  • Open Terminal
  • remote login to Jaylah: ssh uher@jaylah
  • navigate to rawdata folder: cd /shared/uher/FORBOW/rawdata/
  • start pipeline script: nohup ./_1_scripts/FORBOW_2_create_niftis.sh 101_C >nohup_dcm2niix_100_C_20190411.txt 2>&1 &
  • monitor script is running with ps command: ps aux | grep '100_C' or htop command ('q' to quit htop)

Check /shared/uher/FORBOW/rawdata/101_C_20190320/NIFTIS/ for output files, and confirm the /QC/_qc_report.html shows all sequences properly.

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