[caret-users] Palette editing
Alex Fornito
fornitoa at unimelb.edu.au
Sat May 10 02:51:37 CDT 2008
Great. Thanks for your help Donna. I downloaded the snapshot and it now
works.
> 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.
When mapping as paint, I was given no option to use AFM or MFM in the old
version. This option is contained in the new snapshot. I'm therefore
presuming it tried to automatically map to each individual.
> * The Edit paint names should show more than one name, if you mapped
> a ROI volume with more than one intensity.
Again, I'm not sure exactly why this occurred, but I figure it has something
to do with the way it was mapping the file.
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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