[caret-users] Palette editing
Alex Fornito
fornitoa at unimelb.edu.au
Mon May 12 04:33:11 CDT 2008
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#area
> 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/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.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
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>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
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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
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