[caret-users] Palette editing

Fri May 9 11:33:21 CDT 2008

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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>
>   