| FSL MEDx Menu
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The FMRIB Software Library (FSL) is a collection of analysis
tools. Many of these can be accessed by the user via extensions of the
MEDx menu system, under the FSL 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)