Hi Binyam,
That border/borderproj files in that spec file don't include the Core6
landmarks. If you really want them, you could download this borderproj
and bordercolor file:
Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.PALS-B12-SPHERE.borderproj
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6334050
ForSPHERICAL.REGISTRATION_Human.Class3.bordercolor
http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057515
Use File: Open Data File to load the bordercolor first, then the
borderproj file.
But if you're trying to orient yourself to the different sulci, then
another way of doing this might be to view your ROI paint regions, but
also have the
def_to_PALS_B12.LR_Human.colin.Cerebral.L.COMPOSITE.clean.71785.paint
and Human.Cerebral.COMPOSITE_OrbFrontClusters.areacolor files loaded.
Then, when you click on a node or voxel in your ROI, the ID window will
spit out lots of information about that node, e.g.:
Node 38255
Main Window Inflated XYZ: 15.0824, -7.7470, 68.5119 Distance: 32.0371
View Window 2 Inflated XYZ: 15.0824, -7.7470, 68.5119 Distance: 32.0371
Section: 80
Lat/Lon PALS-B12.LR Latitude-Longitude: 2.1453 105.0355
Lat/Lon deformed Human Colin LEFT: -11.2868 102.4004 Atlas Lat/Lon
deformed Human Colin LEFT: -11.2868 102.4004
Paint: LOBE.FRONTAL SUL SUL.CeS MOTOR ??? ??? BROD.4 LANDMARK.Brodmann_4
Shape: -15.4029 -0.0788
The Paint: ... SUL.CeS ... tells you this node is in the central
sulcus. The comment (click on ? button to the right of the Paint radio
buttons on the D/C: Overlay/Underlay - Surface menu) for the deformed
Sulcal ID - Human.colin.L column lists the abbreviations for the sulci.
On 04/19/2006 10:16 AM, Binyam Nardos wrote:
Hi Donna,
Please see inline responses.
Thanks for your help,
Binyam
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of Donna Dierker
Sent: Wed 4/19/2006 8:35 AM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] help needed
Hi Binyam,
See inline responses below.
On 04/18/2006 06:28 PM, Binyam Nardos wrote:
Dear Caret support,
Just started using Caret and I have what might be some elementary
questions for you. I have been trying to make the central sulcus
landmark appear in my fiducial and inflated surfaces that I've mapped
regions of interest on. However, I can't seem to be able to get it to
show, I tried loading all the border data files that I could find in
the PALS folder but the only thing I can get to show up are the lobe
markers(the border files for the central sulcus marker do show up in
the display control window so I'm thinking they are loaded); I also
tried playing with the border colors(specifically those for the
central sulcus marker) but still couldn't get it.
Which spec file are you using? If you got it from sumsdb.wustl.edu, do
you know the directory or archive ID, so I can find it quickly? If not,
then perhaps just the name of the spec file will help. I assume you're
using a publicly available PALS_B12 dataset, rather than a surface you
reconstructed and registered of your own.
Here's the spec file that I am using: Human.PALS_B12.LEFT_HEM.with-COLIN-DATA.73730 and it's in the PALS_Left_Atlas directory that I got from the sums db.
I'm trying out the suggestion you made below.
One more question: I have a volume anatomy file that I've loaded
regions of interest as functional volume files. They show up fine but
I was wondering if there was a way to make each individual region
appear in a different color. Now i've been able to do this while
mapping regions on a fiducial surface by defining a different area
color for each region, is the same thing possible in the volume
anatomy view.?
There is a way to do this -- at least if your paint/ROI
intensities/indices are ordered sequentially (i.e., 1, 2, 3, ...). If
not, then I'm not sure how to do this. Back on 9/2005, a user wanted to
map the AAL ROIs to PALS, but it's intensity-to-parcel scheme looked
like this (116 labels):
FAG Precentral_L 2001
FAD Precentral_R 2002
F1G Frontal_Sup_L 2101
...
VER8 Vermis_8 9150
VER9 Vermis_9 9160
VER10 Vermis_10 9170
The trouble is that the paint index to paint name mapping is stored in
the AFNI .HEAD file like this:
type = string-attribute
name = LUT_NAMES
count = 423
'???~???_not_used~GYRAL~SUL.STS~SUL.AS~SUL.SF~SUL.ITS~SUL.PoCeS~SUL.PoSubCeS~SUL.CeS~SUL.IPrCeS~SUL.pITS~SUL~SUL.IFS~SUL.IPS~SUL.AOS~SUL.OTS~CENTRAL~SUL.intFS~SUL.SPrCeS~SUL.FOS~SUL.MFS~SUL.TOrbS~SUL.LOS~SUL.FMS~SUL.SFS~SUL.CoS~SUL.TOS~SUL.SupPS~SUL.RhS~CALCARINE~MEDIAL.WALL~SUL.CaSd~SUL.OrbS~SUL.HF~SUL.CaSv~SUL.POS~SUL.CiSmr~SUL.CiS~SUL.SSS~SUL.SubPS~SUL.OlfS~SUL.ILS~SUL.SRS~SUL.ISS~SUL.MPrCeS~SUL.PaCeS~SUL.IRS~SUL.LuS~
The ordinal position of the name corresponds to the intensity (first is
intensity=1; second is intensity=2, and so on). But for the AAL volume,
we'd need 2000 bogus names just to get to the first real AAL label,
whose intensity is 2001.
I'm not sure how you get this info into Caret using the GUI; in the
past, I've simply edited the .HEAD file with a text editor (I know,
naughty Donna, but the AFNI police probably already have warrants out
for us for using a non-standard attribute such as LUT_NAMES;-).
Much appreciated,
Binyam Nardos
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--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see
http://home.att.net/~donna.hanlon for details.)
