MCSTRIP: Minneapolis Consensus Strip - V1.6

McStrip processing stages: raw, coarse mask, thresh mask, BSE mask, McStrip mask

Corresponding author: Dr. Kelly Rehm ()

McStrip: Request Download | Install and Run | Set up Parameter File

NOTE: new requirements regarding BSE

What it does:

McStrip (Minneapolis Consensus Strip) is a hybrid method for removing skull and scalp from a T1-weighted MRI brain volume. The output is a binary mask that includes cortical grey matter, white matter, ventricular CSF, and some subarachnoid CSF.   Experiments have shown the hybrid mask to be a closer match to manual strips than the masks of any of its component methods (see references below).

Features:

• Operates on ANALYZE format volumes (8 and 16 bit integers).
• Computes final and four intermediate brain masks which are made by each method in the hybrid algorithm.
• A tuning program is provided to assist in adjusting operating parameters to suit your datasets.
• Runs on PseudoColor and TrueColor display systems.
• Can be set up to run a batch of volumes.
  

Requirements:

• Requires IDL5.5 or higher as either a development or runtime license.  The IDL6.0 Virutal Machine (it's free!) may also be used.  Obtain IDL from Research Systems Inc. at  http://www.rsinc.com/
  
• Requires AIR5.0 or higher.  Obtain this from Dr. Roger Woods at http://bishopw.loni.ucla.edu/AIR5/
• BSE2 or BSE3. This software is part of BrainSuite  http://neuroimage.usc.edu/
  but is no longer available as a separately compiled module. We cannot distribute BSE, we suggest you contact the author David Shattuck.
• Requires 4.9 MBytes disk space for software, 27 MBytes for template files, and a working area of ~8 times the size of a subject volume.
• The download bundle also includes an example volume and the expected results: total size is 45 MBytes (unpacked),  14MBytes for the compressed tarfile.
  

Release History:

• Prior release was 1.1, the New Release is version 1.6.
• Savesets for IDL versions 5.5a, 5.6 and 6.0 are provided; these savesets can be run using a development license or the IDL Virtual Machine.
• Source code is provided.
  

Notes:

• The saveset for IDL6.0 has been tested on a Windows platform.
  
• I do not have access to a MacIntosh platform, but I have been told that the savesets seem to run ok.
• Subject volumes are expected to be in ANALYZE format.   Because the volume orientation code in ANALYZE headers tends to be used inconsistently (if it is used at all)  McStrip will accept a 6-character string describing the layout of a volume.  Under the "Tuning" option there is a step for determining the appropriate string.
  
• I wrote an extensive HELP document to explain how I would set parameters for a new collection of volumes.
  

How to get it:

• Use this REQUEST FORM to request the software.

Installing and using McStrip
Setting parameters in McStrip

Supporting programs:

• REVIEW_MASK (also from this site) lets you scan through your MRI volume in side-by-side unmasked and masked versions.  If you choose to, you may apply the binary mask to the volume and save the result.
• EDITMAN (also from this site) is a manual editor you can use to fix up bits of  a mask that were wrong.  If you have lots of time on your hands you can also use it to draw a completely new mask!
  

Reference:

If you use McStrip in publications, please cite the following:

• Rehm K, Schaper K, Anderson J,  Woods R, Stoltzner S, Rottenberg D.  Putting our heads together: a consensus approach to brain/non-brain segmentation in T1-weighted MR volumes. NeuroImage, 22(3):1262-1270, 2004.

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Page last updated October 13, 2004.