/usr/share/doc/fslview-doc/html/fmri.html is in fslview-doc 4.0.1-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 | <html>
<head>
<link rel="stylesheet" title="normal" type="text/css" href="fslview.css">
<title>Viewing FMRI</title>
<head>
<body>
<h3>Viewing FMRI Data</h3>
<p>FSLView is able to load in FEAT output, and plot as timeseries the
data versus the fitted model (and partial model fits), and also show
the cluster tables produced by FEAT. Start by loading a 4D functional
data set - for example, open <i>filtered_func_data</i> from a
<i>something.feat</i> FEAT output directory.
<p>The displayed volume can be changed with the <i > Volume
SpinBox</i> on the <a href="cursor.html" name"cursor">Cursor
Toolbar</a>. The functional data can also be animated by pressing
the <i >Movie</i> button <img valign=middle src="movie.png">. This
automatically increments the <i >Volume SpinBox</i> and has the effect
of showing all the volumes sequentially and looping back to the first
volume when all volumes have been shown.
<p>You probably also want to load in thresholded zstat images as
colour overlays - for example, press <i>File -> Add</i> and select
<i>thresh_zstat1</i> to load in.
<p>To view timeseries plots of the FMRI data, select the 4D image
(e.g., <i>filtered_func_data</i>) in the <a
href="imagelist.html">Image List</a> and select <i >View ->
Timeseries</i>. Note that FSLView will probably have already opened
this for you, if you started by loading in "filtered_func_data".
<p>A graph will be opened that shows the timeseries plot of the
currently selected voxel. Clicking on the image with the left mouse
button will update the plot with the timeseries of the new cursor
position.
<p>To see the fitted model timeseries, click on the <i>No
model</i> menu button, and select <i>Full model only</i> to view the full
fitted model. To see the partial fit relating to a single EV in the
model, click on the relevant <i>PE</i> menu option. To see the partial
fit relating to a contrast, select the appropriate <i>COPE</i> option.
<p>If you click on the <i>-μ</i> button the data will get
demeaned for plotting, and now if you press the <i>%</i> button, you can
view the timeseries scaled as % signal change.
<p>You can also view the activation cluster tables produced by
FEAT. Press <i>View -> Cluster Browser</i> and you can then select which
zstatistic cluster table to view. If you click on a row in the table,
the cursor in the image viewer will jump to the position of the
maximum zstat value in that cluster.
<!-- <p> -->
<!-- To permanantly keep the current plot on the graph press the -->
<!-- <i >Add series</i> button at the top of the graph.(the -->
<!-- icon is a plus sign) The timeseries plot will now remain on the -->
<!-- graph. The cursor can now be used to add further plots to the graph -->
<!-- while the selected plots remain. -->
<!-- </p> -->
<!-- <p> -->
<!-- The active plot is drawn in green and the inactive plots are drawn in -->
<!-- blue. Clicking the mouse on an inactive plot will make the plot -->
<!-- active and will move the image cursor to the plot's coordinates. -->
<!-- Clicking on the <i >Remove Series</i> button (the icon -->
<!-- is a minus sign) will cause the active plot to be removed from the -->
<!-- graph. -->
<!-- </p> -->
</body>
</html>
|