[caret-users] Palette editing
Donna Dierker
donna at brainvis.wustl.edu
Fri May 9 16:18:20 CDT 2008
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#areaColor
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/comd/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.ali
>>>>> 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.PoSubCe
>>>>> 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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>>>>>
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>>>>
>>>>
>>>
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