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 http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC)
In addition, the algorithm also needs ImageMagick to be installed on your computer (see http://www.imagemagick.org/).
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 https://dicom.offis.de/dcmtk.php.en) and the LAPACK — Linear Algebra PACKage (http://performance.netlib.org/lapack/). In that case, adjust the paths at your local machine for the set variables at the beginning of the makefile.Download ]