Cli Preproc

This module provides a Command-line interface (CLI) for preprocessing imaging data to produce regional PET Time-Activity Curves (TACs) and prepare data for parametric imaging analysis.

The user must provide:

• The sub-command. Options: ‘weighted-sum’, ‘motion-correct’, ‘register-pet’, or ‘write-tacs’.

• Path to PET input data in NIfTI format. This can be source data, or with some preprocessing such as registration or motion correction, depending on the chosen operation.

• Directory to which the output is written.

• The name of the subject being processed, for the purpose of naming output files.

• 3D imaging data, such as anatomical, segmentation, or PET sum, depending on the desired preprocessing operation.

• Additional information needed for preprocessing, such as color table or half-life.

Examples

• Auto Crop:

petpal-preproc auto-crop -i /path/to/input_img.nii.gz -o petpal_crop.nii.gz -t 0.05

• Windowed Motion Correction:

petpal-preproc motion-correct -i /path/to/input_img.nii.gz -o petpal_moco.nii.gz --window-size 120 --transform-type QuickRigid

• Register to anatomical:

   petpal-preproc register-pet -i /path/to/input_img.nii.gz -o petpal_reg.nii.gz --motion-target 0 600 --anatomical /path/to/anat.nii.gz


* Write regional tacs:

petpal-preproc write-tacs -i /path/to/input_img.nii.gz -p sub-001 -o /tmp/petpal_tacs -s /path/to/segmentation.nii.gz -l perlcyno -x

• Write regional tacs, deprecated:

petpal-preproc write-tacs -i /path/to/input_img.nii.gz -o /tmp/petpal_tacs --segmentation /path/to/segmentation.nii.gz --label-map-path /path/to/dseg.tsv

• Half life weighted sum of series:

petpal-preproc weighted-series-sum -i /path/to/input_img.nii.gz -o petpal_wss.nii.gz --start-time 1800 --end-time 7200

• SUVR Image:

petpal-preproc suvr -i /path/to/input_img.nii.gz -o petpal_suvr.nii.gz --segmentation /path/to/segmentation.nii.gz --ref-region 1

• Gaussian blur image:

petpal-preproc gauss-blur -i /path/to/input_img.nii.gz -o petpal_blur.nii.gz --blur-size-mm 8

• Divide image by scale factor:

petpal-preproc rescale-image -i /path/to/input_img.nii.gz -o petpal_rescale.nii.gz --scale-factor 1000

• Warp image to atlas:

   petpal-preproc warp-pet-atlas -i /path/to/input_img.nii.gz -o petpal_reg-atlas.nii.gz --anatomical /path/to/anat.nii.gz --reference-atlas /path/to/atlas.nii.gz

* Crop segmentation to PET FOV:

.. code-block:: bash

    petpal-preproc seg-crop -i /path/to/input_img.nii.gz -o petpal_cropped_seg.nii.gz --segmentation /path/to/segmentation.nii.gz

See also

• image_operations_4d - module used for operations on 4D images.

• motion_corr - module for motion correction tools.

• register - module for MRI and atlas registration.

Attributes

_PREPROC_EXAMPLES_

Functions

_add_common_args(→ None)	Adds common arguments ('--input-img', '--out-img') to a provided ArgumentParser
_generate_args(→ argparse.ArgumentParser)	Generates command line arguments for method main().

Module Contents

petpal.cli.cli_preproc._PREPROC_EXAMPLES_ = Multiline-String

Show Value

"""
Examples:
  - Auto crop:
    petpal-preproc auto-crop -i /path/to/input_img.nii.gz -o petpal_crop.nii.gz -t 0.05
  - Windowed moco:
    petpal-preproc motion-correct -i /path/to/input_img.nii.gz -o petpal_moco.nii.gz --window-size 120 --transform-type QuickRigid
  - Register to anatomical:
    petpal-preproc register-pet -i /path/to/input_img.nii.gz -o petpal_reg.nii.gz --motion-target 0 600 --anatomical /path/to/anat.nii.gz
  - Write regional tacs:
    petpal-preproc write-tacs -i /path/to/input_img.nii.gz -p sub-001 -o /tmp/petpal_tacs -s /path/to/segmentation.nii.gz -l perlcyno -x
  - Write tacs, deprecated:
    petpal-preproc write-tacs-old -i /path/to/input_img.nii.gz -o /tmp/petpal_tacs --segmentation /path/to/segmentation.nii.gz --label-map-path /path/to/dseg.tsv
  - Half life weighted sum of series:
    petpal-preproc weighted-series-sum -i /path/to/input_img.nii.gz -o petpal_wss.nii.gz --start-time 1800 --end-time 7200
  - SUVR:
    petpal-preproc suvr -i /path/to/input_img.nii.gz -o petpal_suvr.nii.gz --segmentation /path/to/segmentation.nii.gz --ref-region 1
  - Gauss blur:
    petpal-preproc gauss-blur -i /path/to/input_img.nii.gz -o petpal_blur.nii.gz --blur-size-mm 8
  - Divide image by scale factor:s
    petpal-preproc rescale-image -i /path/to/input_img.nii.gz -o petpal_rescale.nii.gz --scale-factor 1000
  - Warp to atlas:
    petpal-preproc warp-pet-atlas -i /path/to/input_img.nii.gz -o petpal_reg-atlas.nii.gz --anatomical /path/to/anat.nii.gz --reference-atlas /path/to/atlas.nii.gz
  - SUV:
    petpal-preproc suv -i /path/to/input_img.nii.gz -o petpal_suv.nii.gz --weight 75 --dose 250 --start-time 1200 --end-time 3600
  - Crop segmentation image to PET FOV:
    petpal-preproc seg-crop -i /path/to/input_img.nii.gz -o petpal_cropped_seg.nii.gz --segmentation /path/to/segmentation.nii.gz
  - Add eroded white matter region to segmentation image:
    petpal-preproc eroded-wm -i /path/to/input_segmentation.nii.gz -o petpal_seg_with_eroded_wm.nii.gz
  - Apply brain mask to PET image:
    petpal-preproc brain-mask-pet -i /path/to/input_img.nii.gz -o petpal_brain_masked.nii.gz --atlas $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz --mask $FSLDIR/data/standard/MNI152_T1_1mm_brain_mask.nii.gz
"""