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  • minc-stuffs (formerly mice-minc-tools)

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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
#mincminc_label_opsManipulate label (segmentation) files

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minc_label_ops

Anchor
minc_label_ops
minc_label_ops

Usage:

Code Block
none
none
minc_label_ops [options] input_labels.mnc output_labels.mnc

# example: consider the following scenario, you have two atlases
# atlas1.mnc and atlas2.mnc and you want to add labels 56 and 99
# from atlas1.mnc to atlas2.mnc. Run the following:

minc_label_ops --select 56,99 atlas1.mnc atlas1_labels_56_99.mnc
minc_label_ops --merge atlas1_labels_56_99.mnc atlas2.mnc atlas2_with_labels_from_altas1.mnc