[caret-users] Palette editing
Donna Dierker
donna at brainvis.wustl.edu
Mon May 12 11:46:19 CDT 2008
Make sure you have primary overlay selected as Metric on the D/C menu,
and that you have the right column selected. If so, save your metric
results, if needed, and upload the metric here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
Upload the volume you mapped, too.
On 05/12/2008 11:40 AM, Alex Fornito wrote:
> Thanks John.
> It seems that no matter what I do, I am unable to visualize the problem.
> This makes me think something has gone wrong with the mapping, although it
> seems to proceed fine when I run it.
> I can overlay the volume on say, the avg152 in FSLview, and have used
> exactly the same procedure that I have previoulsy in Caret to successfully
> map other volumes that have a similar format (albeit with different
> intensity ranges).
> Can you recommend a way of troubleshooting this problem?
> Thanks,
> Alex
>
>
> On 12/05/2008 14:28, "John Harwell" <john at brainvis.wustl.edu> wrote:
>
>
>> Alex,
>>
>> On one of Display Control's Metric pages is a group of options named
>> "Color Mapping". Its default value is "Auto Scale" in which the most
>> positive metric value is mapped to +1 in the palette, the zero metric
>> is mapped to zero in the palette, and the most negative metric is
>> mapped to -1 in the palette. If your data truly ranges from ranges
>> from zero to 300, you could stick with auto scale. If not, change the
>> "Color Mapping" to "User Scale" and set the "Pos Min/Max" values to
>> 0.0 and 300.0. If you palette has red at 0.33, orange at 0.66, and
>> yellow at 1.0, metric values of 0 to 100 are assigned red, metric
>> values of 100 to 200 are assigned orange, and metric values of 200 to
>> 300 are assigned yellow.
>>
>> Also see
>> "http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/dialogs/display_contro
>> l_dialog.html#MetricSettingsPage
>> ".
>>
>> John
>>
>> On May 12, 2008, at 4:33 AM, Alex Fornito wrote:
>>
>>
>>> Hi again,
>>> As a second step, I would like to map a volume onto the PALS
>>> surface in
>>> which each voxel in the volume is assigned a value between 0 and
>>> 300. I
>>> would like to visualise it as some sort of heatmap, such that lower
>>> values
>>> are red, gradually moving through orange and yellow to represent
>>> higher
>>> values.
>>>
>>> I have tried editing the palettes through the GUI, but it seems the
>>> values
>>> assigned to colours must be between -1 and +1. Is there any way to
>>> create
>>> palettes for arbitrary scales, or another way to visualize the image
>>> as
>>> decsribed above?
>>>
>>> Thanks again for your help,
>>> Alex
>>>
>>>
>>> On 09/05/2008 22:18, "Donna Dierker" <donna at brainvis.wustl.edu> wrote:
>>>
>>>
>>>> Hi Alex,
>>>>
>>>> You are missing something: The all important Attributes: Paint:
>>>> Generate Colors for paints without colors. I want to say you must
>>>> have
>>>> it, but that's overstating it just a bit. It's well worth
>>>> downloading
>>>> the latest snapshot here:
>>>>
>>>> http://brainvis.wustl.edu/pub/caret/
>>>> login pub
>>>> password download
>>>>
>>>> If you'd really rather not, the you can still map the ROI as paint,
>>>> and
>>>> then save the resulting paint file; convert it to ASCII using the
>>>> endangered File: Convert data file formats option; and then use a
>>>> text
>>>> editor to extract the paint names from it. Then, manually create an
>>>> area color file to map the paint names to RGB colors:
>>>>
>>>> http://brainmap.wustl.edu/caret/caret_help/file_formats/file_formats.html#ar
>>>> ea
>>>> Color
>>>>
>>>> I'm puzzled over two things in your message:
>>>>
>>>> * The 12 PALS subjects' paint columns makes sense only if you have
>>>> loaded an existing PALS paint file such as
>>>> Human.PALS_B12.IDsulci_B1-12_RIGHT.clean.73730.atlas.paint, but even
>>>> then, after mapping your ROI paint volume, you should have a 13th (or
>>>> more) column for what you just mapped.
>>>>
>>>> * The Edit paint names should show more than one name, if you
>>>> mapped
>>>> a ROI volume with more than one intensity.
>>>>
>>>> I have detailed all the steps in what I did, in hopes that you can
>>>> pinpoint the problem on your end (after upgrading to the latest
>>>> snapshot):
>>>>
>>>> Download the CARET_TUTORIAL_SEPT06.zip dataset:
>>>>
>>>> http://sumsdb.wustl.edu/sums/directory.do?id=6585200
>>>>
>>>> Extract the zip file and cd CARET_TUTORIAL_SEPT06 directory.
>>>>
>>>> Launch caret and select PALS_B12.RIGHT.DEMO.73730.spec.
>>>>
>>>> Load scenes and double-click scene 13.
>>>>
>>>> File: view current files
>>>> Click X to clear the loaded paint file
>>>> Note: I think your 12 loaded paint columns may have been preloaded
>>>> from
>>>> an existing PALS paint file.
>>>> Click X to clear both loaded average fiducial coord files
>>>> Note: These are the wrong space; we need the AFNI coord here.
>>>> Yours may
>>>> vary.
>>>>
>>>> Toolbar: Spec: Open
>>>> Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_AFNI.clean.73730.coord
>>>>
>>>> Attributes: Map volume to surface
>>>> Paint ROI or probabilistic atlas data
>>>> Add volumes from disk: TTatlas.nii
>>>> Map to Caret
>>>> select Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_AFNI.clean.
>>>> 73730.coord
>>>> accept remaining defaults
>>>>
>>>> Attributes: Paint: Edit paint names, if desired
>>>>
>>>> Attributes: Paint: Generate colors for paints with no colors
>>>>
>>>> D/C: Overlay/Underlay: Surface
>>>> Primary overlay Paint
>>>> Select desired display column
>>>> D/C: Paint Main
>>>> Display Color key
>>>>
>>>> File: Save Data File: Paint
>>>> File: Save Data File: Area Color File
>>>>
>>>> Donna
>>>> PS I assume you will attend OHBM2008, right? John and David will
>>>> be there.
>>>>
>>>> On 05/09/2008 02:25 PM, Alex Fornito wrote:
>>>>
>>>>> Sorry, I can't seem to follow.
>>>>>
>>>>> I map the volume to the PALS surface as a Paint ROI. I then get 12
>>>>> options
>>>>> in the paint D/C dialog, corresponding to a mapping to the 12
>>>>> cases in the
>>>>> PALS atlas. Is it possible to obtain one, as per the AFM option?
>>>>>
>>>>> If I go to Attributes > Paint > Edit paint names, all I have is an
>>>>> option to
>>>>> change one name.
>>>>>
>>>>> After I change the name, there is no option under Attributes >
>>>>> Paint that
>>>>> corresponds to Generate colours for paint colours without colours.
>>>>> The
>>>>> options I have under Attributes > Paint are:
>>>>>
>>>>> Assign nodes within displayed borders.
>>>>> Cleanup paint names.
>>>>> Clear all or part of paint file.
>>>>> Convert pain column to paint volume.
>>>>> Edit paint names.
>>>>>
>>>>> Am I missing something?
>>>>> I'm sing version Caret 5.51
>>>>>
>>>>> Thanks again,
>>>>> Alex
>>>>>
>>>>> On 09/05/2008 17:57, "Donna Dierker" <donna at brainvis.wustl.edu>
>>>>> wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Hi Alex,
>>>>>>
>>>>>> Cool! John has added some features that make this a little easier.
>>>>>>
>>>>>> Go ahead and map your volume as ROI paint. If mapping to atlas
>>>>>> doesn't
>>>>>> give you the options you'd like, simply start with a spec file
>>>>>> that has
>>>>>> the PALS average fiducial surfaces in it, and map to Caret while
>>>>>> the
>>>>>> average fiducial surface is loaded.
>>>>>>
>>>>>> Then you won't be able to see the paint overlay yet, because no
>>>>>> color is
>>>>>> associated with the automatically assigned paint name. First, do
>>>>>> Attributes: Paint: Edit Paint Names and properties to update the
>>>>>> paint
>>>>>> names to something more meaningful. Then, do Attributes: Paint:
>>>>>> Generate colors for paint without colors. Save both the paint
>>>>>> and area
>>>>>> color files: The paint assigns nodes to paint names; the area
>>>>>> color
>>>>>> maps paint names to RGB colors. If you change the name of the
>>>>>> paint,
>>>>>> change it in both. If you want to do this with perl, sed, or awk,
>>>>>> convert the paint file to ASCII first (using either File: Convert
>>>>>> data
>>>>>> file formats or the caret_command utility).
>>>>>>
>>>>>> Make sure D/C overlay/underlay surface has paint as overlay, and
>>>>>> I like
>>>>>> D/C: Paint Main : Display Color key.
>>>>>>
>>>>>> A capture of the mapped TTatlas is attached.
>>>>>>
>>>>>> Donna
>>>>>>
>>>>>> On 05/09/2008 11:33 AM, Donna Dierker wrote:
>>>>>>
>>>>>>
>>>>>>> Hi Alex,
>>>>>>>
>>>>>>> Would you mind uploading your ROI volume
>>>>>>> (http://pulvinar.wustl.edu/cgi-bin/upload.cgi)? It has been
>>>>>>> quite a
>>>>>>> while since I've done this, and I know the gotchas are in this
>>>>>>> case
>>>>>>> more case/data dependent than most (e.g., life will be easier if
>>>>>>> your
>>>>>>> intensities increment like 1, 2, 3, rather than 5, 10, 15).
>>>>>>> Next best
>>>>>>> thing is a histogram of the values.
>>>>>>>
>>>>>>> Meanwhile, I'll dig TTatlas out of my AFNI distribution, so I
>>>>>>> can try
>>>>>>> mapping it.
>>>>>>>
>>>>>>> Donna
>>>>>>>
>>>>>>> On 05/09/2008 11:26 AM, Alex Fornito wrote:
>>>>>>>
>>>>>>>
>>>>>>>> Hi Donna,
>>>>>>>> You're right, I am trying to overlay something like the AAL,
>>>>>>>> where each
>>>>>>>> 'intensity' in the region corresponds to a different ROI.
>>>>>>>>
>>>>>>>> I would like to load it into Caret so that each ROI gets a
>>>>>>>> different
>>>>>>>> colour.
>>>>>>>> It sounds like I should indeed load it as a paint rather than
>>>>>>>> metric
>>>>>>>> file,
>>>>>>>> although when I go to Attributes > Map Volume to Surface and
>>>>>>>> load as
>>>>>>>> Paint
>>>>>>>> (ROI) or probabistic data, I get 12 options in the paint
>>>>>>>> selection
>>>>>>>> area in
>>>>>>>> the D/C, corresponding to the mapping for each of the cases in
>>>>>>>> the PALS.
>>>>>>>> When I try to visualize any of them, I can't see anything.
>>>>>>>>
>>>>>>>> I would just like the AFM mapping, but there does not seem to
>>>>>>>> be an
>>>>>>>> option
>>>>>>>> for selecting this with Paint, as their is with metric. In the
>>>>>>>> summary
>>>>>>>> before proceeding with the mapping however, it does state that
>>>>>>>> AFM
>>>>>>>> will be
>>>>>>>> performed.
>>>>>>>> Am I missing something?
>>>>>>>>
>>>>>>>>
>>>>>>>> On 09/05/2008 14:47, "Donna Dierker" <donna at brainvis.wustl.edu>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Hi Alex,
>>>>>>>>>
>>>>>>>>> What you describe is more like what we call a ROI paint
>>>>>>>>> volume, like
>>>>>>>>> the
>>>>>>>>> AAL map shown here:
>>>>>>>>>
>>>>>>>>> http://http://www.sph.sc.edu/comd/rorden/template.htmlwww.sph.sc.edu/co
>>>>>>>>> md
>>>>>>>>> /r
>>>>>>>>> ord
>>>>>>>>>
>>>>>>>>> en/template.html
>>>>>>>>>
>>>>>>>>> When you map in Caret, you have the option of mapping
>>>>>>>>> functional as
>>>>>>>>> metric, or Paint (ROI); you want the latter.
>>>>>>>>>
>>>>>>>>> The tricky bit is that NIfTI (to my imperfect knowledge)
>>>>>>>>> doesn't yet
>>>>>>>>> support incoding of ROI lookup tables. (John will correct me
>>>>>>>>> if I'm
>>>>>>>>> wrong.) The only two ways I know to do this, using Caret, are
>>>>>>>>> with
>>>>>>>>> WUNIL 4dfp ifh files, or with AFNI volumes, using a VElab
>>>>>>>>> (non-standard)
>>>>>>>>> LUT tag in the HEAD file. An example of the latter is in the
>>>>>>>>> Sept 2006
>>>>>>>>> tutorial dataset http://sumsdb.wustl.edu/sums/directory.do?id=6585200)
>>>>>>>>> :
>>>>>>>>>
>>>>>>>>> CARET_TUTORIAL_SEPT06/PALS_B12.B1-12.BOTH-HEMS.PROB-
>>>>>>>>> ATLAS_IDsulci.paint.a
>>>>>>>>> li
>>>>>>>>> gn_
>>>>>>>>>
>>>>>>>>> 222+orig.HEAD
>>>>>>>>>
>>>>>>>>> type = string-attribute
>>>>>>>>> name = LUT_NAMES
>>>>>>>>> count = 423
>>>>>>>>> '???~???
>>>>>>>>> _not_used
>>>>>>>>> ~GYRAL~SUL.STS~SUL.AS~SUL.SF~SUL.ITS~SUL.PoCeS~SUL.PoSub
>>>>>>>>> Ce
>>>>>>>>> S~S
>>>>>>>>>
>>>>>>>>> UL.CeS~SUL.I
>>>>>>>>> PrCeS
>>>>>>>>> ~
>>>>>>>>> SUL
>>>>>>>>> .pITS~SUL~SUL.IFS~SUL.IPS~SUL.AOS~SUL.OTS~CENTRAL~SUL.intFS~SUL.
>>>>>>>>> SP
>>>>>>>>> rCe
>>>>>>>>>
>>>>>>>>> S~SUL.FOS~SU
>>>>>>>>> L
>>>>>>>>> .MFS
>>>>>>>>> ~
>>>>>>>>> SUL
>>>>>>>>> .TOrbS~SUL.LOS~SUL.FMS~SUL.SFS~SUL.CoS~SUL.TOS~SUL.SupPS~SUL.RhS
>>>>>>>>> ~C
>>>>>>>>> ALC
>>>>>>>>>
>>>>>>>>> ARINE~MEDIAL
>>>>>>>>> .WALL
>>>>>>>>> ~
>>>>>>>>> SUL
>>>>>>>>> .CaSd~SUL.OrbS~SUL.HF~SUL.CaSv~SUL.POS~SUL.CiSmr~SUL.CiS~SUL.SSS
>>>>>>>>> ~S
>>>>>>>>> UL.
>>>>>>>>>
>>>>>>>>> SubPS~SUL.Ol
>>>>>>>>> fS~SUL.ILS~SUL.SRS~SUL.ISS~SUL.MPrCeS~SUL.PaCeS~SUL.IRS~SUL.LuS~
>>>>>>>>>
>>>>>>>>> Here, the ordinal position of the ROI/paint name corresponds
>>>>>>>>> to the
>>>>>>>>> intensity value in the volume.
>>>>>>>>>
>>>>>>>>> You then map these paint names to RGB colors using an ordinary
>>>>>>>>> Caret
>>>>>>>>> area color file.
>>>>>>>>>
>>>>>>>>> Donna
>>>>>>>>>
>>>>>>>>> On 05/08/2008 10:44 AM, Alex Fornito wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>> Thanks for the feedback, although I need it to overlay a
>>>>>>>>>> volume on the
>>>>>>>>>> surface. I essentially have a volume-based template
>>>>>>>>>> comprising several
>>>>>>>>>> thousand ROIs, with each ROI being assigned a distinct
>>>>>>>>>> 'intensity'.
>>>>>>>>>> I have
>>>>>>>>>> imported the volume-based template into Caret as a metric
>>>>>>>>>> file, and
>>>>>>>>>> would
>>>>>>>>>> like to be able to visualize it such that each volume
>>>>>>>>>> 'intensity'
>>>>>>>>>> (corresponding to a different ROI) is a different colour.
>>>>>>>>>> I imagine the appearance would be much like the image you
>>>>>>>>>> sent, but
>>>>>>>>>> somewhat
>>>>>>>>>> coarser, since its not a nodal resolution.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> From what I understand, a paint file can't be used to colour
>>>>>>>>>>> code
>>>>>>>>>>> a metric
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>> file?
>>>>>>>>>> Is there another way of achieving my goal that I'm unaware of?
>>>>>>>>>>
>>>>>>>>>> Thanks again,
>>>>>>>>>> Alex
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 06/05/2008 15:13, "John Harwell" <john at brainvis.wustl.edu>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Alex,
>>>>>>>>>>>
>>>>>>>>>>> If you generated a palette file with that many colors I
>>>>>>>>>>> think it
>>>>>>>>>>> would
>>>>>>>>>>> be slow to load and slot to make the color assignments. A
>>>>>>>>>>> better
>>>>>>>>>>> alternative is to use this python script to generate an RGB
>>>>>>>>>>> paint
>>>>>>>>>>> file
>>>>>>>>>>> containing random colors. You will need to adjust the
>>>>>>>>>>> "numberOfNodes"
>>>>>>>>>>> variable in the script to match your dataset.
>>>>>>>>>>>
>>>>>>>>>>> ---------------------------------------------------------------------
>>>>>>>>>>> --
>>>>>>>>>>> --
>>>>>>>>>>> ---
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> ----------------------------
>>>>>>>>>>>
>>>>>>>>>>> #!/usr/bin/python
>>>>>>>>>>> #
>>>>>>>>>>> # Create an RGB paint file with random colors
>>>>>>>>>>> #
>>>>>>>>>>> import os
>>>>>>>>>>> import random
>>>>>>>>>>> import sys
>>>>>>>>>>>
>>>>>>>>>>> #
>>>>>>>>>>> # Name of RGB Paint file and number of nodes in the file
>>>>>>>>>>> #
>>>>>>>>>>> rgbPaintFileName = "random.RGB_paint"
>>>>>>>>>>> numberOfNodes = 71723
>>>>>>>>>>>
>>>>>>>>>>> #
>>>>>>>>>>> # Create an RGB paint file with random colors
>>>>>>>>>>> #
>>>>>>>>>>> file = open(rgbPaintFileName, 'w')
>>>>>>>>>>> file.write("tag-version " + str(2) + "\n")
>>>>>>>>>>> file.write("tag-number-of-nodes " + str(numberOfNodes) + "\n")
>>>>>>>>>>> file.write("tag-number-of-columns " + str(1) + "\n")
>>>>>>>>>>> file.write("tag-BEGIN-DATA\n");
>>>>>>>>>>> for i in range(numberOfNodes):
>>>>>>>>>>> node = str(i)
>>>>>>>>>>> red = str(random.random() * 255.0)
>>>>>>>>>>> green = str(random.random() * 255.0)
>>>>>>>>>>> blue = str(random.random() * 255.0)
>>>>>>>>>>> line = node + " " + red + " " + green + " " + blue + "\n"
>>>>>>>>>>> file.write(line)
>>>>>>>>>>>
>>>>>>>>>>> file.close()
>>>>>>>>>>>
>>>>>>>>>>> ---------------------------------------------------------------------
>>>>>>>>>>> --
>>>>>>>>>>> --
>>>>>>>>>>> ---
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> ----------------------------
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> -----------------------------------
>>>>>>>>>>> John Harwell
>>>>>>>>>>> john at brainvis.wustl.edu
>>>>>>>>>>>
>>>>>>>>>>> Department of Anatomy and Neurobiology
>>>>>>>>>>> Washington University School of Medicine
>>>>>>>>>>> 660 S. Euclid Ave Box 8108
>>>>>>>>>>> Saint Louis, MO 63110
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On May 6, 2008, at 4:46 AM, Alex Fornito wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> Hi,
>>>>>>>>>>>> I need to generate a custom palette for viewing some masks.
>>>>>>>>>>>> I need
>>>>>>>>>>>> it to
>>>>>>>>>>>> contain 5000-10000 colours, in no particular order or
>>>>>>>>>>>> pattern. I.e.,
>>>>>>>>>>>> they
>>>>>>>>>>>> can be random, they just need to provide some kind of visual
>>>>>>>>>>>> distinction
>>>>>>>>>>>> between 5000-10000 points on the cortical surface. I can
>>>>>>>>>>>> see how to
>>>>>>>>>>>> manually
>>>>>>>>>>>> edit palettes, but it does not seem feasible to repeat the
>>>>>>>>>>>> process
>>>>>>>>>>>> 1000s of
>>>>>>>>>>>> times. Is there a simple way to generate a palette with
>>>>>>>>>>>> several
>>>>>>>>>>>> 1000s of
>>>>>>>>>>>> random colours so that it can be used in Caret?
>>>>>>>>>>>> Thanks for your help,
>>>>>>>>>>>> Alex
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> caret-users mailing list
>>>>>>>>>>>> caret-users at brainvis.wustl.edu
>>>>>>>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> caret-users mailing list
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>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> caret-users mailing list
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>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>> _______________________________________________
>>>>>> caret-users mailing list
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>>>>>>
>>>>>>
>>>>>
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>>>>
>>> --
>>>
>>> Alex Fornito
>>> CJ Martin Post-Doctoral Fellow
>>> Brain Mapping Unit
>>> Department of Psychiatry
>>> University of Cambridge
>>> Addenbrooke¹s Hospital
>>> Hills Rd, Cambridge
>>> UK CB2 2QQ
>>>
>>> Email: af397 at cam.ac.uk
>>> Phone: +44 (0) 1223 336587
>>> Fax: +44 (0) 1223 336581
>>>
>>> Australian Details:
>>>
>>> Melbourne Neuropsychiatry Centre
>>> National Neuroscience Facility
>>> Levels 1 & 2, Alan Gilbert Building
>>> 161 Barry St
>>> Carlton South 3053
>>> Victoria, Australia
>>>
>>> Email: fornitoa at unimelb.edu.au
>>> Phone: +61 3 8344 1861
>>> Fax: +61 3 9348 0469
>>>
>>>
>>>
>>> _______________________________________________
>>> caret-users mailing list
>>> caret-users at brainvis.wustl.edu
>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>
>>>
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