[caret-users] Palette editing
Donna Dierker
donna at brainvis.wustl.edu
Fri May 9 11:57:11 CDT 2008
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/comd/rord
>>>
>>> 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.align_
>>>
>>> 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.PoSubCeS~S
>>>
>>> UL.CeS~SUL.I
>>> PrCeS~SUL.pITS~SUL~SUL.IFS~SUL.IPS~SUL.AOS~SUL.OTS~CENTRAL~SUL.intFS~SUL.SPrCe
>>>
>>> S~SUL.FOS~SU
>>> L.MFS~SUL.TOrbS~SUL.LOS~SUL.FMS~SUL.SFS~SUL.CoS~SUL.TOS~SUL.SupPS~SUL.RhS~CALC
>>>
>>> ARINE~MEDIAL
>>> .WALL~SUL.CaSd~SUL.OrbS~SUL.HF~SUL.CaSv~SUL.POS~SUL.CiSmr~SUL.CiS~SUL.SSS~SUL.
>>>
>>> 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
>>>>>>
>>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>
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>>
>>
>
>
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