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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 data are 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 dicom data in the rawdata folder into nifti format and copy the nifti data up one directory into Biotic3T and create and organize the subject folders in a specific way to make later preprocessing possible.

  1. Open the terminal.
  2. Navigate to the _scripts folder in /shared/uher/FORBOW_Brain/neuro_data/Biotic3T/
  3. Drag the 0_convert_dcm2niix.sh script into the terminal
  • alternatively, cd into the _scripts folder and type 0 and click tab to autocomplete
  1. In terminal, after the script path, type subject IDs that need to be converted (space separated), for example 032_A 033_A 031_B
  2. Click enter to run script on specified subjects.

Check /shared/uher/FORBOW_Brain/neuro_data/Biotic3T/ for the subjects specified. There should be new folders with the subject IDs. In those folders you will find the unprocessed folder which has all the nifti files ready for preprocessing, and a log folder where preprocessing pipeline will log all the steps and spit out any errors.

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