Arterial Spin Labeling (ASL) FAQs


The Center currently supports 2 resting-state ASL methods for whole-brain baseline CBF:

1. FAIR (pulsed ASL)

2. MP-PCASL(pseudocontinuous ASL)

Brief descriptions of each method are included in the tables below.

A detailed instruction manual that covers data acquisition, reconstruction and CBF quantification can be downloaded here for FAIR and MP-PCASL.

Data reconstruction, CBF quantification, and field map correction software (Matlab-based):

Recent Updates: 

03/22/2011:  Updated spiralfmap2 to version 3.1. Added parallel processing capability to significantly reduce processing time. For more information, please refer to readme file included with the download. 

01/04/2011:  Updated spiralfmap2 to version 2.1. This update incorporates registration of field map to functional data (geometrical correction) prior to off-resonance correction. For more information, please refer to readme file included with the download. 

12/07/2010:  Updated SENSErc from v2.0 to v3.0. The update includes a bug fix associated with processing 12x and 15x data as well as added support for FSL version 4.0.4.

08/30/2010:  Updated spiralfmap2 to version 1.2. This version automatically selects center slices for fieldmap correction if the fieldmap slice coverage is larger than that of the ASL data.

04/27/2010:  Added spiralfmap2v1.1. Use this for processing ASL data and field map data acquired at the Center field map protocols.

04/20/2010:  Version upgrade for CBF from v3.3 to v3.4. This version has a built-in support for Multi-Phase PCASL (MPPCASL).

04/20/2010:  Version upgrade for SENSErc: v1.3. to v2.0. This version has a support for 20x and is also compatible with pre-14x software platforms.

04/12/2010:  All matlab programs were developed in Matlab version 2009a, and may not work in older matlab versions.  

09/19/2008: FSL 4.1.0 no longer supports ANALYZE format, therefore will not work with any of the Center offered software.  Please do NOT upgrade to FSL4.1.0 at this time. Use FSL4.0 or 3.x !

09/12/2008: The software has been updated to be compatible with FSL4.0.  This update is  backward-compatible with FSL3x.

Download links: 

SENSErc3.0.tar - SENSE recon code for all software platforms (20x, 15x, 14x, and 12x)

CBFv3.4.tar- CBF quantification (backward compatible with pre-14x software platforms and added support for whole brain MPPCASL ASL)

spiralfmap2v3.1.tar- Field map correction algorithm for 20x/14x software platforms. Provides geometrical correction (registration) of field map and target images.  Also provides parallel processing capability. Refer to readme file included with the download for more information. Supports field map data acquired with older and new protocols. For more details on available field map protocols at the Center, click here.

If you would like to schedule a training session for baseline whole-brain perfusion using ASL, please contact David Shin.

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FAIR Protocol

Protocol name

Brain_perfusion_4S Brain_perfusion_SS (Single-shot Spiral)

Description

  • FAIR ASL
  • Spiral-out readout
  • 4 interleaves
  • gr recon and optional SENSE recon
  • Scan time (6:40min) + calibration scans (1:00min)

 

  • FAIR ASL
  • Spiral-out readout
  • Single shot
  • gr recon
  • Scan time (4:10min) + calibration scans (1:00min)

 

Pros

  • Reduced drop out in the frontal and medial-temporal lobe regions.
  • Reduced T2* blurring
  • Shorter scans
  • Fast reconstruction (< 5minutes)

Cons

  • Longer scans
  • Slow reconstruction  in Matlab (> 4 hrs ) when using the optional SENSE recon program
  • Increased signal drop out in the frontal/ medial- temporal lobe regions.
  • Increased T2* blurring

 

Recommended use

Recommended for all studies.

The optional SENSE recon is strongly recommended for a more robust performance.

Recommended for motor and visual cortex studies that desire faster scans and data processing.


MP-PCASL Protocol

Protocol Name MP_Brain_perfusion_SS (Single-shot Spiral)
Description:
  • 8-phase PCASL
  • Spiral-out readout
  • gr recon
  • Scan time (4:54 min) + mincon calibration scan (30 sec) + TOF (1:43 min)
  • Separate CSF scan is no longer required (it is incorporated into the acquisition)
Pros:
  • High SNR
  • Well-controlled temporal bolus leading to robust CBF quantification
Cons:
  • Increased signal bunching and dropouts in the frontal/ medial- temporal lobe regions.
  • Increased T2* blurring

However, these can be greatly reduced by field map correction.
Recommended Use:
  • Recommended for resting-state whole-brain ASL studies that need high SNR.
  • The optional field map correction scans (2:12 min) are strongly recommended for reduced signal bunching and dropouts in the frontal/medial temporal lobes and reduced T2* blurring.
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Software version
 Additional functionality
CBFv1.0
 Original release
CBFv2.0 Anatomical can be used for CSF voxel identification
CBFv2.1 Fixed small bug in v2.0
CBFv2.2 Performs checks, e.g. that ASL and CSF runs acquired with same prescan. Also handles other tagging schemes aside from PASL
CBFv2.3 Fixed small bug in v2.2
CBFv2.4 ASL and CSF scans acquired with different R1 values can be processed; correction is applied. User is warned to check acquisition protocol
CBFv3.0 (1) Performs motion correction of ASL data. (2) Checks system's software versions. (3) Easier CSF slice selecting when using anatomical. (4) User is asked to check alignment of CSF scan relative to the anatomical (if used)
CBFv3.1 Compatible with data collected on GE 3Tand 1.5T scanners
CBFv3.2
 Made compatible with FSL4 and fixed small bugs
CBFv3.3 Added Gaussian filter option to smooth the ouput CBF brik for the 4 interleave data if desired. Default is off.
CBFv3.4 Added support for MR750 and whole brain MPPCASL ASL
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As part of the Cerebral Blood Flow Biomedical Informatics Research Network (CBFBIRN) Project, we provide an online database that you can use to upload, process, store and retrieve your ASL data.

Please click on the following link to go to the CBFBIRN Project site:

https://cbfbirn.ucsd.edu/site/

By taking advantage of the services provided by this project, you will no longer need to keep up with the latest software updates and process your data offline.

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