MINC/Scripts

Scripts These scripts can all be downloaded from packages volrot volrot is will rotate a MINC volume about the centre of the volume. This script would typically be used to sort out orientation issues with a MINC volume. A typical usage to rotate a volume 90 degrees about the x axis would be as such: volrot -x_rotation 90 input.mnc output.mnc nlpfit nlpfit performs a hierarchical nonlinear fit of one volume to another. This is done via fitting one image to the other using progressively finer nonlinear grid functions. minctracc from the mni_autoreg package is used to perform the fits. The default fitting profile consists of a 16mm, 8mm and 4mm fit. As part of the fitting the volumes are also blurred with progressively smaller FWHM kernels, this is done in order to reduce the chances of a fit a particular level falling into local minima. The default fit profile can be changed by creating a fit config file and using the -config_file option. An example (the default fit config) is below: @conf = ( {'step' => 16, 'blur_fwhm' => 8, 'iterations' => 3, }, {'step' => 8, 'blur_fwhm' => 4, 'iterations' => 2, }, {'step' => 4, 'blur_fwhm' => 4, 'iterations' => 2, }, );