ASL pipeline inventory
This OSIPI TF 1.1. ASL inventory list ASL pipelines features and requirements self-assessed by their developers using an online questionnaire.
If you want to have your pipeline added, either fill the questionnaire or contact TF 1.1 leaders j.petr@hzdr.de or sudiptod@pennmedicine.upenn.edu.
The tables below contain information about
- Basic pipeline information
- Basic requirements and inputs
- Main processing features
- Data already processed with the pipeline
Table 1. Contact
Ease of use | |||||||
Pipeline Name | Institution | Download | Publication/Website | Author's name | M N U A L | S O U R C E | G U I |
ASAP | Erasmus MC | ✓ | ✓ | ||||
ASLtbx | University of Pennsylvania | ✓ | ✓ | ✓ | |||
ASL-MRICloud | Johns Hopkins School of Medicine | ✓ | ✓ | ||||
aslm | University of Zurich | ✓ | ✓ | ✓ | |||
ASLPrep | University of Pennsylvania | ✓ | ✓ | ||||
BASIL | University of Oxford, University of Nottingham | ✓ | ✓ | ✓ | |||
CereFlow | Translational MRI LLC | ✓ | ✓ | ||||
CLINICAL ASL-CVR | University Medical Center Utrecht | ✓ | |||||
ENABLE | Sunnybrook Research Institute | Zahra Shirzadi, Brad MacIntosh | ✓ | ✓ | |||
ExploreASL | Amsterdam UMC | ✓ | ✓ | ✓ | |||
FASL (Functional ASL) | University of MIchigan | ✓ | ✓ | ||||
Iris pipeline | Erasmus MC | ✓ | ✓ | ||||
LOFT-CBF | LOFT, University of Southern California | Kay Jann, Danny Wang, Chenyang Zhao | ✓ | ||||
milxASL | CSIRO | Amir Fazlollahi | |||||
mjdASL | Vanderbilt University Medical Center | ✓ | ✓ | ||||
nordicICE (nICE) | Oslo University Hospital | ✓ | ✓ | ||||
Philips 3D ASL | Philips Healthcare | Philips Healthcare | |||||
Quantiphyse (ASL) | University of Oxford, University of Nottingham | ✓ | ✓ | ||||
SCRUB-ASL | University of Pennsylvania | ✓ | ✓ | ||||
Super-selective pCASL CBF | UKSH Kiel,UKE Hamburg | ✓ | |||||
VANDPIRE | Vanderbilt University Medical Center | Daniel Arteaga, Manus Donahue | ✓ | ✓ | |||
Andrea Federspiel | University of Bern | Andrea Federspiel | ✓ | ||||
Author contact information and affiliation, link for publication and download, availability: On request , commercial license .
Table 2. Requirements
Basic requirements on the operating system (MacOS, Linux , Windows, cloud), software (Matlab, FSL, SPM, Python), and data input types, MR vendors (Agilent, GE healthcare, Philips healthcare, Siemens healthineers, United imaging - other vendors might work but were not tested). All pipelines were developed and tested to work with human brain scans, further tested functionality is provided for different organs or for animal use in the last column.
Input data type | ||||||||||
Pipeline Name | Supported MR vendors | Operating system | Software Requirement | A N A L Y Z E | B I D S | D I C O M | E N H - D C M | N I F T I | P A R / R E C | Organ, animal |
ASAP |
| ✓ | ✓ | ✓ | ||||||
ASLtbx | ✓ | ✓ | ||||||||
ASL-MRICloud |
| ✓ | ||||||||
aslm |
| ✓ | ||||||||
ASLPrep |
|
| ✓ | |||||||
BASIL |
| ✓ | ✓ | Mice/rats | ||||||
CereFlow |
| ✓ | ✓ | |||||||
CLINICAL ASL-CVR |
|
| ✓ | ✓ | ✓ | ✓ | ||||
ENABLE |
|
| ✓ | ✓ | Monkeys | |||||
ExploreASL | ,(GUI), none (compiled) | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |||
FASL (Functional ASL) | ✓ | ✓ | ||||||||
Iris pipeline |
| ✓ | ✓ | ✓ | ✓ | |||||
LOFT-CBF | ✓ | ✓ | ||||||||
milxASL |
|
| ✓ | ✓ | Prostate | |||||
mjdASL |
|
| ✓ | ✓ | ✓ | Kidney | ||||
nordicICE (nICE) |
| ✓ | ✓ | ✓ | ||||||
Philips 3D ASL |
|
| scanner | ✓ | ✓ | |||||
Quantiphyse (ASL) | N/A | ✓ | Mice/rats | |||||||
SCRUB-ASL | ✓ | ✓ | ✓ | ✓ | ||||||
Super-selective pCASL CBF |
|
| Im.Proc.Tbx | ✓ | ||||||
VANDPIRE |
|
| ✓ | ✓ | ✓ | Kidney | ||||
Andrea Federspiel |
|
| ✓ | |||||||
Table 3. Features
Main features concerning the labeling type (pCASL: pseudo-continuous ASL, PASL: pulsed ASL, s-PLD: single post-labeling delay (PLD), m-PLD: multi-PLD, L-L: Look-Locker, T-enc: time or Hadamard encoded; VS: vessel/super selective), use of partial volume correction (PVC), denoising (temporal, spatial, deep learning (DL)); output space of the resulting maps (ASL space, T1 space, MNI space); output of regional values (whole brain, GM, manually provided ROI, standard atlases); and a presence of a quality-control (QC) report or images are provided to facilitate subject exclusion.
Sequence type | Denoising | ||||||||||||||
Pipeline name | P A S L | P C A S L | S - P L D | M - P L D | L - L | T - E N c | V S | f A S L | P V C | T E M P | S P A T L | D L | Output space | Regional evaluation | QC |
ASAP | ✓ | ✓ | ✓ |
| |||||||||||
ASLtbx | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| |||||
ASL-MRICloud | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| ✓ | |||||||
aslm | ✓ |
| |||||||||||||
ASLPrep | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||||||||
BASIL | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| |||||
CereFlow | ✓ | ✓ | ✓ | ✓ |
| ✓ | |||||||||
CLINICAL ASL-CVR | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |||||||
ENABLE | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| ✓ | |||||||
ExploreASL | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |||||||
FASL (Functional ASL) | ✓ | ✓ | ✓ | ✓ | |||||||||||
Iris pipeline | ✓ | ✓ | ✓ | ✓ |
| ✓ | |||||||||
LOFT-CBF | ✓ | ✓ | ✓ | ✓ | ✓ | ||||||||||
milxASL | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||||||||
mjdASL | ✓ | ✓ | ✓ | ✓ | |||||||||||
nordicICE (nICE) | ✓ | ✓ | ✓ |
| ✓ | ||||||||||
Philips 3D ASL | ✓ | ✓ | |||||||||||||
Quantiphyse (ASL) | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| ✓ | ||||||
SCRUB-ASL | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ||||||
Super-selective pCASL CBF | ✓ | ✓ | |||||||||||||
VANDPIRE | ✓ | ✓ | ✓ | ✓ | ✓ | ||||||||||
Andrea Federspiel | ✓ | ✓ | ✓ |
| |||||||||||
Table 4. Experience
This table approximates the actual use of the pipeline in practice. It lists how many different studies/trials/datasets were processed by the pipeline; how many human brain and non-brain, and animal scans were processed by the pipeline. For studies, the developers were able to choose from options 0, 1-5, 5-10, 10-20, 20-50, 50-100, and 100+. For scans, the options were 0, 1-10, 10-100, 100-1000, 1000-10000, 10000+. Note that the numbers were subjectively self-assessed and are thus rough estimates only.
Pipeline Name | Studies | Human brain scans | Human non-brain scans | Animal scans |
ASAP | 10-20 | 1,000-10,000 | 0 | 0 |
ASLtbx | 100+ | 10,000+ | 0 | 0 |
ASL-MRICloud | N/A | 10,000+ | 0 | 0 |
aslm | 5-10 | N/A | 0 | 0 |
ASLPrep | 100+ | 10,000+ | 0 | 0 |
BASIL | 50-100 | 1,000-10,000 | 10-100 | 10-100 |
CereFlow | 20-50 | 10,000+ | 0 | 0 |
CLINICAL ASL-CVR | 5-10 | 100-1,000 | 10-100 | 0 |
ENABLE | 10-20 | 1,000-10,000 | 0 | 0 |
ExploreASL | 50-100 | 10,000+ | 0 | 0 |
FASL (Functional ASL) | 5-10 | 10-100 | 0 | 0 |
Iris pipeline | 5-10 | 1,000-10,000 | 0 | 0 |
LOFT-CBF | 10-20 | 1,000-10,000 | 0 | 0 |
milxASL | 5-10 | 1,000-10,000 | 0 | 0 |
mjdASL | 20-50 | 100-1,000 | 10-100 | 0 |
nordicICE (nICE) | 1-5 | 10-100 | 0 | 0 |
Philips 3D ASL | 100+ | 10,000+ | 0 | 0 |
Quantiphyse (ASL) | 1-5 | 10-100 | 0 | 1-10 |
SCRUB-ASL | 20-50 | 10,000+ | 0 | 0 |
Super-selective pCASL CBF | 1-5 | 10-100 | 0 | 0 |
VANDPIRE | 20-50 | 100-1,000 | 10-100 | 0 |
Andrea Federspiel | 10-20 | 100-1,000 | 0 | 0 |