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DOC: More info about calling a asltk script (Getting Started page)
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acsenrafilho committed Nov 26, 2024
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Expand Up @@ -115,4 +115,46 @@ At the moment, there are the following scripts avaliable:
1. `cbf.py`: Python script focused on calculating CBF/ATT maps using pCASL images. This script is based on the `CBFMapping` class.
2. `te_asl.py`: Python script focused on calculating T1 relaxation exchange time between Blood and Grey-Matter (T1blGM) map using pCASL multi-TE ASL images. This script is based on the `MultiTE_ASLMapping` class.

Here's an example of how to call the cbf.py script to calculate CBF/ATT maps using pCASL images:

```bash
python -m asltk.scripts.cbf --pcasl ./path/to/pcasl_image.nii.gz --m0 ./path/to/m0_image.nii.gz --output ./path/to/output_directory
```

In this example:

- `--pcasl` specifies the path to the pCASL image.
- `--m0` specifies the path to the M0 image.
- `--output` specifies the directory where the output CBF/ATT maps will be saved.

!!! tip
Make sure to replace `./path/to/pcasl_image.nii.gz`, `./path/to/m0_image.nii.gz`, and `./path/to/output_directory` with the actual paths to your pCASL image, M0 image, and desired output directory, respectively.

Anyway, the complete description on how to call a `asltk` script can be checked using the `--help` command:

```bash
python -m asltk.scripts.cbf --help

usage: CBF/ATT Mapping [-h] --pld PLD [PLD ...] --ld LD [LD ...] [--verbose] pcasl m0 [mask] [out_folder]

Python script to calculate the basic CBF and ATT maps from ASL data.

Required parameters:
pcasl ASL raw data obtained from the MRI scanner. This must be the basic PLD ASL MRI acquisition
protocol.
m0 M0 image reference used to calculate the ASL signal.
out_folder The output folder that is the reference to save all the output images in the script. The
images selected to be saved are given as tags in the script caller, e.g. the options --cbf_map
and --att_map. By default, the TblGM map is placed in the output folder with the name
tblgm_map.nii.gz
--pld PLD [PLD ...] Posts Labeling Delay (PLD) trend, arranged in a sequence of float numbers
--ld LD [LD ...] Labeling Duration trend (LD), arranged in a sequence of float numbers.

Optional parameters:
mask Image mask defining the ROI where the calculations must be done. Any pixel value different
from zero will be assumed as the ROI area. Outside the mask (value=0) will be ignored. If not
provided, the entire image space will be calculated.
--verbose Show more details thoughout the processing.
```

Additional scripts can be added in the `asltk` library, by the community contribution. If it is your interest, then go to the [developing scripts](contribute.md) section at the developer guidelines.

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