Man Pages in mia-tools

Section 1: Executable programs or shell commands

mia-2davgmasked.1

Evaluate average intensities of an image series.

mia-2dbinarycombine.1

Combine two binary images.

mia-2dcost.1

Evaluate the similarity between two 2d images.

mia-2ddeform.1

Transform a 2d image by means of a vector field.

mia-2ddistance.1

Distance between binary masks.

mia-2deval-transformquantity.1

Evaluate derivative of a transformation

mia-2dfluid.1

Fluid dynamic 2d registration

mia-2dforce.1

Registering force between two 2d images.

mia-2dfuzzysegment.1

A fuzzy c-means segmentation of a 2d image

mia-2dgrayimage-combine-to-rgb.1

Combine gray scale images to an rgb image.

mia-2dgroundtruthreg.1

Registration of a series of 2d images

mia-2dimagecombine-dice.1

Evaluate the dice index between two binary 2d images.

mia-2dimagecombiner.1

Combine two 2d images.

mia-2dimagecreator.1

Create a synthetic 2d image.

mia-2dimagefilter.1

Run filters on a 2d image.

mia-2dimagefilterstack.1

Run filters on a series of 2d images.

mia-2dimagefullstats.1

Evaluate some stats over an image.

mia-2dimageregistration.1

Run a 2d image registration.

mia-2dimageselect.1

Select one image from a multi-record file.

mia-2dimageseries-maximum-intensity-projection.1

Evaluate maximum per-pixel intensities of an image series.

mia-2dimagestats.1

Evaluate some statistics of a 2d image.

mia-2dlerp.1

Linearly combine two 2d images.

mia-2dmany2one-nonrigid.1

Registration of a series of 2d images

mia-2dmultiimageto3d.1

Convert a 2d multi-record image to a 3d image.

mia-2dmultiimagevar.1

Evaluate the intensity variation of pixels in a series of images.

mia-2dmyocard-ica.1

Run an ica analysis on a series of 2d images

mia-2dmyocard-icaseries.1

Run an ica analysis on a series of 2d images

mia-2dmyocard-segment.1

Work in progress

mia-2dmyoica-full.1

Run a registration of a series of 2d images.

mia-2dmyoica-nonrigid.1

Run a registration of a series of 2d images.

mia-2dmyoica-nonrigid-parallel.1

Run a registration of a series of 2d images.

mia-2dmyoica-nonrigid2.1

Run a registration of a series of 2d images.

mia-2dmyoicapgt.1

Run a registration of a series of 2d images.

mia-2dmyomilles.1

Run a registration of a series of 2d images.

mia-2dmyoperiodic-nonrigid.1

Run a registration of a series of 2d images.

mia-2dmyopgt-nonrigid.1

Run a registration of a series of 2d images.

mia-2dmyoserial-nonrigid.1

Run a serial registration of a series of 2d images.

mia-2dmyoseries-compdice.1

Evaluate the dice index between segmentations.

mia-2dmyoseries-dice.1

Evaluate the dice index between segmentations.

mia-2dmyoset-all2one-nonrigid.1

Non-linear registration of a series of 2d images.

mia-2dsegcompare.1

Evaluate the hausdorff distance between segmentations.

mia-2dseghausdorff.1

Evaluate the hausdorff distance between segmentations.

mia-2dsegment-ahmed.1

Run a fuzzy c-means segmentation of a 2d image.

mia-2dsegment-fuzzyw.1

Run a fuzzy c-means segmentation of a 2d image.

mia-2dsegmentcropbox.1

Evaluate a crop-box around a manual segmentation.

mia-2dsegseriesstats.1

Evaluate time-intensity curves in masked regions of image series.

mia-2dsegshift.1

Translate a segmentation by the given amount.

mia-2dsegshiftperslice.1

Translate a segmentation by the given amount.

mia-2dseries-mincorr.1

Evaluate minimal correlation of time-intensity curves.

mia-2dseries-sectionmask.1

Evaluate masks from a segmentation.

mia-2dseries-segdistance.1

Evaluate mean distance between segmentations.

mia-2dseries2dordermedian.1

Evaluate time-intensity median 2nd order derivative of a series.

mia-2dseries2sets.1

Combine images of a series to sets.

mia-2dseriescorr.1

Evaluate the time-intensity correlation in a series of images.

mia-2dseriesgradMAD.1

Evaluate the time-intensity gradient mad in a series of images.

mia-2dseriesgradvariation.1

Evaluate the time-intensity gradient variation in a series of images.

mia-2dserieshausdorff.1

Evaluate hausdorff distance between segmentation sets.

mia-2dseriessmoothgradMAD.1

Evaluate pixel-wise time-intensity gradient of a 2d image series.

mia-2dseriestovolume.1

Create a 3d volume from a segmentation series.

mia-2dstackfilter.1

Filter a series of 2d images in a 3d fashion.

mia-2dto3dimage.1

Combine a series of 2d images to a volume.

mia-2dto3dimageb.1

Combine a series of 2d images to a volume.

mia-2dtrackpixelmovement.1

Track positions in 2d

mia-2dtransform.1

Transform a 2d image.

mia-2dtransformation-to-strain.1

Green strain tensor.

mia-3dbinarycombine.1

Combine two binary images.

mia-3dbrainextractT1.1

Extract the brain from a 3d t1 mri head image.

mia-3dcombine-mr-segmentations.1

Combine segmentations.

mia-3dcost.1

Evaluate similarity of two 3d images.

mia-3dcost-translatedgrad.1

Evaluate the cost gradient between two images and convert it to a spline representation.

mia-3dcrispsegment.1

Label segmentation according to probabilities.

mia-3ddeform.1

Transform a 3d image by means of a vector field.

mia-3ddistance.1

Evaluate the distance between two binary shapes.

mia-3ddistance-stats.1

Evaluate distance statistics for two labeled images.

mia-3deval-transformquantity.1

Evaluate derivative of a transformation

mia-3dfield2norm.1

Evaluate the norm image of a 3d vector field.

mia-3dfluid.1

Fluid dynamic 3d registration

mia-3dforce.1

Evaluate the registration force between two 3d images.

mia-3dfuzzysegment.1

Fuzzy c-means segmentation of a 3d image.

mia-3dgetsize.1

Print the dimensions of a 3d image.

mia-3dgetslice.1

Extract slices from a 3d image.

mia-3dimageaddattributes.1

Add attributes to the meta data of a 3d image.

mia-3dimagecombine.1

Combine two 3d images.

mia-3dimagecreator.1

Create a synthetic 3d image.

mia-3dimagefilter.1

Filter a 3d images.

mia-3dimagefilterstack.1

Filter a series of 3d images.

mia-3dimageselect.1

Select one image from multi-image file.

mia-3dimagestats.1

Evaluate some image statistics.

mia-3disosurface-from-stack.1

Extract an ist-surface froma a 3d image.

mia-3disosurface-from-volume.1

Extract an ist-surface froma a 3d image.

mia-3dlandmarks-distances.1

Evaluate per landmark distances between 3d landmark sets.

mia-3dlandmarks-transform.1

Transform 3d landmark positions.

mia-3dlerp.1

Linearly combine two 3d images.

mia-3dmany2one-nonrigid.1

Registration of series of 3d images

mia-3dmaskseeded.1

Mask an area by seeded region growing

mia-3dmotioncompica-nonrigid.1

Non-linear registration of a series of 3d images.

mia-3dnonrigidreg.1

Non-linear registration of 3d images

mia-3dnonrigidreg-alt.1

Non-linear registration of 3d images.

mia-3dprealign-nonrigid.1

Registration of a series of 3d images.

mia-3drigidreg.1

Linear registration of 3d images.

mia-3dsegment-ahmed.1

Run a fuzzy c-means segmentation of a 3d image.

mia-3dserial-nonrigid.1

Serial registration of 3d images.

mia-3dseries-track-intensity.1

Track intensities of pixels in series of 3d images.

mia-3dtrackpixelmovement.1

Track positions in 3d

mia-3dtransform.1

Transform a 3d image.

mia-3dtransform2vf.1

Create vectorfield from a transformation.

mia-3dvectorfieldcreate.1

3d vector field creation.

mia-3dvf2transform.1

Convert a 3d vectorfield from a 3d transformation.

mia-3dvfcompare.1

Compare two vectorfields.

mia-cmeans.1

C-means classification of a histogram.

mia-filenumberpattern.1

File name number pattern analysis

mia-labelsort.1

Create sorted histogram mapping

mia-meshdistance-to-stackmask.1

Evaluate the distance between a binary shape given as reference and a mesh.

mia-meshfilter.1

Run filters on a 3d mesh.

mia-multihist.1

Histogram of a series of 2d images

mia-myowavelettest.1

Wavelet based curve analysis

mia-plugin-help.1

Print help about plug-in groups

mia-raw2image.1

Convert raw data into a 2d image

mia-raw2volume.1

Convert raw data into a 3d image

mia-wavelettrans.1

Column wise wavelet transform