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titleminc-stuffs repository

The mice-stuffs package was formerly called MICe-minc-tools are now part of the or mice-minc-tools. The updates to the code can be found on the GitHub page: minc-stuffs github repository. Any updates to the The code can be downloaded and installed from there.

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minc-

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stuffs overview

MICe-minc-tools stuffs is a software package containing disparate command line tools operating on MINC files developed at the Mouse Imaging Centre. The tools are:

Command

Brief Description

#minc_displacement

Create a vector volume containing the displacements at each voxel specified by a transform (.xfm file).

#label_volumes_from_jacobians

Compute the volume of segmented structures given an atlas and Jacobian determinants.

#xfm2tag

Create a tag file from a transform.

#lin_from_nlin

Compute the linear part of a non-linear transform.

#scale_voxels

Multiply values in a file by the combined scale factor of a linear transform.

#smooth_vector

Blur a vector file.

#grid_object_manipulator

Pretty pictures of deformation fields

#add_noise_to_volume

Add normally distributed noise to a volume.

TFCEThreshold-free cluster enhancement

Installation instructions

Get the code here

The C code relies on MINC-2.0.09 or greater installed. #smooth_vector requires python, and #add_noise_to_volume requires R and RMINC, and the rest requires perl, Getopt::Tabular, and mni_perllib.

After untarring the tarball, the The following commands will perform the install:

Code Block
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none
./autogen.sh
./configure --with-minc2 --prefix=/directory/to/install/to --with-build-path=/directory/containing/minc2
make 
make install

python setup.py install --prefix=/directory/to/install/to

Description of included programs.

minc_displacement

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minc_displacement
minc_displacement

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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

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label_volumes_from_jacobians
label_volumes_from_jacobians

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  • 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

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xfm2tag
xfm2tag

Usage:

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An optional argument allows one to specify a mask - the transform will only be evaluated inside the mask.

lin_from_nlin

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lin_from_nlin
lin_from_nlin

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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

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scale_voxels
scale_voxels

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scale_voxels multiplies every voxel in an input volume by the scale factor determined from a linear transform.

smooth_vector

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smooth_vector
smooth_vector

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Blurs a vector volume by separating the vector components, blurring them individually using mincblur, then recombining them.

grid_object_manipulator

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grid_object_manipulator
grid_object_manipulator

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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):

add_noise_to_volume

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add_noise_to_volume
add_noise_to_volume

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