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DICOM → NIfTI (non-BIDS)

What this page tells you

In cnt1 go to /project/imaging_process/programs/run_dcm2niix, unzip the dicoms (unzip '*.zip'), edit the batch script or txt file with input/output paths, and run bash dcm2niix_directory.sh; niftis appear in the output folder.

in the VDI

ssh cnt1

cd /project/imaging_process/programs/run_dcm2niix

  • here you can use either batch_processing or directory_processing
    • directory will go into sub directories within main directory
    • batch will go into all files within directory

for directory_processing

  • edit the dcm2niix_batch.sh text file with input and output path
  • edit the txt file with input and output path

to run code: bash dcm2niix_directory.sh

niftis will show up in the nifti output folder

New-
dicoms need to be unzipped
go to folder and type unzip '*.zip'
all files will unzip