The mice-stuffs package was formerly called MICe-minc-tools are or mice-minc-tools. The updates to the code can be found on the GitHub page: minc-stuffs github repository. The code can be downloaded and installed from there.
minc-stuffs is a software package containing disparate command line tools operating on MINC files developed at the Mouse Imaging Centre. The tools are:
Create a vector volume containing the displacements at each voxel specified by a transform (.xfm file).
Compute the volume of segmented structures given an atlas and Jacobian determinants.
Create a tag file from a transform.
Compute the linear part of a non-linear transform.
Multiply values in a file by the combined scale factor of a linear transform.
Blur a vector file.
Pretty pictures of deformation fields
Add normally distributed noise to a volume.
|TFCE||Threshold-free cluster enhancement|
|#minc_label_ops||Manipulate label (segmentation) files|
Get the code here
The following commands will perform the install:
Description of included programs.
minc_displacement evaluates a transform - linear nonlinear, concatenated, etc - at every voxel of an input file and produces a 4D output volume containing the displacement in x,y,z at every voxel.
label_volumes_from_jacobians produces a list of labels and their volumes from a segmented atlas and a volume of log jacobians. Some important notes:
- The exponent of the input jacobians is taken - it thus has to be a volume of logs of jacobians.
- The atlas volume and the jacobians have to be in the same space with the same sampling - i.e. evaluations take place in voxel coordinates.
xfm2tag takes a transform and an input volume in the space of which the transform can be evaluated and produces a tag file similar in composition to what register would produce after manual registration. This tag file can then be used to create a newer and perhaps simpler transform using tagtoxfm. xfm2tag is the key tool behind lin_from_nlin.
An optional argument allows one to specify a mask - the transform will only be evaluated inside the mask.
lin_from_nlin takes a non-linear transform and an input volume over which the non-linear transform can be evaluated and computes the linear component of the non-linear transform. Options can be used to specify lsq12, lsq9, or lsq6 for the resulting linear transform.
scale_voxels multiplies every voxel in an input volume by the scale factor determined from a linear transform.
Blurs a vector volume by separating the vector components, blurring them individually using mincblur, then recombining them.
grid_object_manipulator uses ray_trace to create pictures of what a deformation grid looks like. Lots of options to control the grid-point spacing, use of overlays, and other ray_trace options. The image below is one example generated by grid_object_manipulator (click on it for a larger image):
What every lab needs - a way to make their images look worse. add_noise_to_volume adds x percent normally distributed noise to an input volume. Needs R with the RMINC library installed.