IntracranialVolume is a C++ pipeline for Linux that utilizes the Minc tools MRI computational package to extract and calculate the Intracranial volume (ICV) from a T1w MRI scan.

The pipeline works with dicom, nifti and minc (.mnc) formats.

Thus, for the program to run, the Minc tools should be installed on your computer (see

In addition, the algorithm also needs ImageMagick to be installed on your computer (see

The algorithm is based on a co-registration of a model brain and a subject brain together through a series of linear and non-linear registration steps.

After the registration transformation from the model brain to the subject brain is calculated, the ICV of the subject is back-calculated from an ICV mask of the model brain.

We provide, code, model brains for 1,5 and 3 Tesla scanner (for adults and kids) and the corresponding ICV masks.

In addition, we provide a compiled command-line based version of the pipeline.

If you will want to compile it yourself (using the provided makefile) you will also need the DICOM toolkit dcmtk (see and the LAPACK — Linear Algebra PACKage ( In that case, adjust the paths at your local machine for the set variables at the beginning of the makefile.

For further questions: Yaron Caspi ( or Hilleke Hulshoff Pol (

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