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FSL MEDx Menu

• FEAT, FMRIB's Easy Analysis Tool.
  
  
• General
  • BET - Brain Extraction, segments brain from non-brain; aids registration etc.
  • FLIRT Linear Registration, automatic, accurate, robust registration.
  • SUSAN Nonlinear Noise Reduction, structure-preserving image noise reduction.
  • Make Image Isometric, resample using trilinear interpolation to give cubic voxels with side length = min(orig side lengths).
  • Concat Transforms, allowing the combination of two saved spatial image transformations
  • Copy Origin, allowing the copying of volume origin and voxel sizes from selected page (see note on page selection) to current page
  • Delayed Folder Saving; you tell the script how long to wait before saving the folder. Then you can set things running (e.g., overnight) and make sure that they get saved.
  • Make Voxel Dimensions Positive; some images come with negative voxel dimensions - this screws up some MEDx functions, including AIR. To make all dimensions positive, use this function. Note that the original image will still exist in the folder.
• Group Operations
  • Group Median
  • Group Do (Generic Operation) pops up a generic group operation script in an editor for the user to enter a page command inside the group loop. Thus an operation (or set of operations) can be applied to each page in a group. ImageScript logging can be used to find out what the script command(s) should be.
  • Scatter Plot from 2 Images produces a Gnuplot plot from a group page containing two volumes of identical data type and dimensionality. At each voxel position the value from the first image and the value from the second image are output as pair of ASCII values to a data file. This file is then displayed in Gnuplot.
• FMRI
  • FEAT
  • Model-Free ANOVA, Stuart's utility for running an ANOVA analysis without specifying a waveform.
  • Statistics Colour Rendering, a tool for rendering colour blobs onto a background image.
  • Signal-to-Noise Ratio, can be used both to measure initial ratio of temporal standard deviation to mean, and also as a test for MC quality.
  • Serial T Test, John O'Doherty's script for running serial T Tests on subgroups of blocks. The relevant image group must be selected as the current page before running this script.
  • Cluster Reporting of % Change, John O'Doherty's script for taking in a thresholded Z score image, a % change image, a mask image and a fused (colour) Z score image with functional image, and producing a new version of the fused image which can be clicked in to find the index number of any cluster; this index can then be used to refer to the cluster table, which includes average % change for each cluster. See note on page selection.
• Graphics / Output
  • Cut 3D Corner, asks the user to draw a rectangle on a 3D image and then deletes this rectangle and all rectangles in the same position in higher slices; normally used to cut a corner out of a 3D image prior to 3D rendering.
  • Cut 3D Corner Shell, similar to Cut 3D Corner, except that only the shell around the deleted cuboid is kept, i.e., data outside the cuboid is also deleted.
  • Rendering Animation, pops up a script in an editor which shows how to save a rotating brain animation to gif format.
  • Rolling Display, displays all the images in the current group in a rolling loop.

Scripts requiring page selection other than the current page: When a script needs (as input) only one page, this is found from the current page selected in MEDx. However, when a script needs as input more than one page, the choosing of these pages is normally achieved using the Page Manager or similar dialog. However, at present, MEDx extensions cannot use this method. Therefore, to select the different images asked for by various interfaces, bring up the Page Manager, select (with left mouse button) a page in the Page Manager, and paste into the relevant box on the new interface (with the middle mouse button)