Christian,
Thanks for your help. Out of curiosity, if I want to have my custom lut
loaded as one of the choices every time I open FSL View, where would I put
it?
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Christian Beckmann
Sent: Saturday, February 03, 2007 7:55 PM
To: [log in to unmask]
Subject: Re: [FSL] Using Overlay and Slicer to Automate Collection of Images
for Figures
Hi,
yes, you can certainly use a custom look up table, it just needs to
be in a format that slicer understands. Examples of valid lookup
tables are in $FSLDIR/etc/luts. These are standard ascii text files
which contain 200 or more color entries (RGB values). The first 100
normally are simply the colors from black to white and encode the way
that the bg image will be rendered. The next 100 values then encode
the colors for the first stats image to be overlayed on top of the
bg. If you only want 4 colors then you still need the 200 entries and
simply use the 100 entries for black-white followed by 25 repetitions
each of the 4 colors that you need. Save this as a new lut file
('custom.lut')
In order to get the desired rendering you then
(i) first use overlay to create a new nifti file which combines the
bg and the classification results
overlay <colour_type> <output_type> [-c] <background_image> <bg_min>
<bg_max> <stat_image_1> <s1_min> <s1_max> [stat_image_2 s2min s2max]
<output_image>
use color_type 1 if you want the color of the overlay barkened/
lightened depending on the brightness of the underlying bg image -
this creates a transparency effect - use 0 for solid colors
you can play around with the following option, I normally use 0 for
floating point
specify the bg image file name
specify the min and max intensity for the bg image (i.e. if bg ranges
from 0 to 100 in intensity, then values of 10 and 90 will render
every voxel <=10 as black and >=90 as white, the rest scaled linearly
within that range. If you use the -a option instead, then overlay
will use the 2nd and 98 percentile of the image range (robust range).
specify the file name of the stats image (e.g. a volume with the same
#voxels and voxel dims as the bg which contains the data you want to
render)
specify the min and max values to be renderd into the lut range
specify the output file name
Overall a call will look like
overlay 0 0 subjects_hr_img -a tracts 1 4 output
(ii) then call slicer with the options required, e.g.
slicer output -l custom.lut -x 0.5 mid_sag.png -y 0.5 mid_cor.png -z
0.5 mid_ax.png
will create 3 PNG files
You can then use pngappend to merge these 3 into a custom image if
you want
hope this helps
christian
On 3 Feb 2007, at 17:08, Matt Glasser wrote:
> I am having some difficulty figuring out how to use overlay and
> slicer to
> automate collection of images for figures. I have a structural
> volume on
> which I want to overlay a volume with some connectivity based seed
> classification probtrack results. I made a custom look up table with
> different colors for values 1, 2, 3, and 4 that I want to use to
> display the
> CBSC results. First, I am wondering if this is even possible to do?
> Second, I'm not really understanding the documentation of overlay.
>
> Thanks,
>
> Matt.
--
Christian F. Beckmann
Oxford University Centre for Functional
Magnetic Resonance Imaging of the Brain,
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/~beckmann/
Phone: +44(0)1865 222551 Fax: +44(0)1865 222717
|