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Example: use bruker2nifti via Command Line Interface

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Sebastiano Ferraris edited this page Dec 17, 2018 · 1 revision

In this example we use the publicly available dataset bruker2nifti_qa (thanks to Mikaël Naveau).

  • <data_folder> contains the study to convert.
  • <destination_folder> is where the converted study will be stored.
  • Please see the Definitions of scan, study and experiment.

Convert a study

Invoke the help of the Command Line Interface:

bruker2nii -h

To convert the study of the example proposed, type:

bruker2nifti -i <data_folder>/raw/McGill_Orientation/a20130329_APM_DEV_Orient.j71 -o <destination_folder> -study_name my_study -nifti_version 1 -qform_code 1 -sform_code 2 -save_human_readable True -correct_slope True -verbose 1

Via the CLI the user can also convert only a single scan invoking bruker2nifti_scan.

Convert a single scan

Via the CLI the user can also convert only a single scan invoking bruker2nifti_scan.

To convert the second scan of the study McGill_Orientation/a20130329_APM_DEV_Orient.j71, type:

bruker2nifti -i <data_folder>/raw/McGill_Orientation/a20130329_APM_DEV_Orient.j71/2 -o <destination_folder> -study_name my_study
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