[caret-users] Palette editing
John Harwell
john at brainvis.wustl.edu
Wed May 21 11:49:31 CDT 2008
Alex,
The color bar value shows only one digit to the right of the decimal
point and the number is rounded.
If you are using one of the recent "caret snapshots", go to the
Display Control's Metric Selection page. Press the "H" button for the
metric data that is displayed. This will display a histogram and list
the range of values for the metric data. If you are using an older
version of caret, the minimum and maximum metric value for the
displayed column are listed on the Display Control's Metric page.
John
On May 21, 2008, at 11:18 AM, Alex Fornito wrote:
> Hi again,
> I was just wondering how the auto scaling is done for visualizating
> metric
> files.
>
> When I overlay a metric file, the autoscale scales it between 0 and
> 0.2 (as
> indicated by the colour bar). However, if I set the User scale to
> between
> these values I get a slightly different result.
>
> Thanks for your help,
> Alex
>
>
>
> On 12/05/2008 17:46, "Donna Dierker" <donna at brainvis.wustl.edu> wrote:
>
>> 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_cont
>>>> ro
>>>> 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
>>>>>>>>>>>>> caret-users at brainvis.wustl.edu
>>>>>>>>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> caret-users mailing list
>>>>>>>>>>> caret-users at brainvis.wustl.edu
>>>>>>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> caret-users mailing list
>>>>>>>> caret-users at brainvis.wustl.edu
>>>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
>>>>>> caret-users mailing list
>>>>>> caret-users at brainvis.wustl.edu
>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>>>
>>>>> --
>>>>>
>>>>> Alex Fornito
>>>>> CJ Martin Post-Doctoral Fellow
>>>>> Brain Mapping Unit
>>>>> Department of Psychiatry
>>>>> University of Cambridge
>>>>> Addenbrooke’s 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
>>>>>
>>>>>
>>>> _______________________________________________
>>>> caret-users mailing list
>>>> caret-users at brainvis.wustl.edu
>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>>
>>>
>>>
>>
>> _______________________________________________
>> caret-users mailing list
>> caret-users at brainvis.wustl.edu
>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
> --
>
> Alex Fornito
> CJ Martin Post-Doctoral Fellow
> Brain Mapping Unit
> Department of Psychiatry
> University of Cambridge
> Addenbrooke’s 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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