us know and we'll draft ad hoc
explanatory comments.
David Van Essen
On Dec 16, 2005, at 11:02 AM, John Harwell wrote:
Erin,
Caret is designed to work with a single hemisphere. We have had some
discussions about loading and viewing both hemispheres simultaneously
but I do not know if that wil
Hi Wichian,
Caret has capabilities for importing and visualizing a variety of
spatially localized data. I am not aware of any groups that have
imported ERP data into Caret, nor am I familiar with the particular
data formats generated from ERP analyses. However, we would like to
encourag
Roland,
If your partial hemisphere does not include the anterior commissure,
it will probably be important to DE-select the Disconnect Hindbrain,
Disconnect Eye and Skull, Cut Corpus Callosum, and Fill Ventricles
options, as these rely on stereotaxic coordinates relative to the AC.
We don
06 00:50, David Van Essen wrote:
Roland,
If your partial hemisphere does not include the anterior commissure,
it will probably be important to DE-select the Disconnect Hindbrain,
Disconnect Eye and Skull, Cut Corpus Callosum, and Fill Ventricles
options, as these rely on stereotaxic coordinates rel
Terry (et al.),
Although the ECHDB is evidently defunct, the data sets you are
interested in (plus much more) are available by alternate routes.
The primary data sets are accessible at a website at the Zilles lab
(and also one at McGill) that is indicated lower down in this
message. In a
Terry,
On Feb 9, 2006, at 11:37 AM, Terry Sewards wrote:
In their description of the cytoarchitectonic map of area 2
Grefkes et al. (2001) show area 2 occupying the rostral bank of the
postcentral sulcus, not extending into the fundus or caudal bank,
but in the
probabilistic maps area 2
Alex,
It's puzzling to me why this is happening. However, when it does
occur you should be able to fix the problem using the Attributes:
Area Colors: Edit Area Colors option. Assuming that the desired area
color name is not there, enter it using the New Color option. Once
you hit the A
Aaron,
Donna's email covers the key technical issues. I have some
clarifications to add regarding the semantics of what we mean by the
term 'fiducial' surface.
We consider that the term 'fiducial' is applicable to ANY surface
configuration that 'captures' the shape of a given hemisphere,
Alex,
One more tidbit:
It occasionally happens that a coordinate file has an incorrect
hemisphere assignment. The easiest way to fix this is to re-save the
coord file and reassign the hemisphere at the time of re-saving. You
can also text-edit the spec file.
David
Also, how and when
Terry,
In Caret 5.3 you can draw 3-D borders on non-flat surfaces, using the
Dimensions: 3D option in the Draw Borders dialog box. Instead of
using the fiducial surface, a highly inflated surface works better
(see below - and is easy to generate if you don't have one already).
Make sure
7; to
[EMAIL PROTECTED]
You can reach the person managing the list at
[EMAIL PROTECTED]
When replying, please edit your Subject line so it is more specific
than "Re: Contents of caret-users digest..."
Today's Topics:
1. Re: Drawing b
Hi Jason,
Donna's email nicely laid out our lab's perspective on several
important issues regarding cortical landmarks and registration. I
will amplify on a few aspects here. The issues that arise in
considering whether the precentral sulcus may be a useful landmark
are linked to the n
Jason,
I suspect that somewhere along the line, the deformed left hemisphere
surfaces got linked to an inappropriate topology file. However, the
atlas spec file you used should be valid - It is a left-right hybrid
target that is viewed with a right hemisphere topology. We have done
man
Terry et al.,
Donna's evaluations and recommendations regarding registration of the
macaque to the PALS atlas are on track - it can indeed be done by a
two-step procedure using existing deformation_map files.
However, this brings home the point that it makes more sense to do a
direct regi
Alex et al.,
The 3-D variability maps for both left and right hemispheres are
available at:
http://sumsdb.wustl.edu:80/sums/archivelist.do?archive_id=6478157
Human.PALS_B12.LR.B_1-12.BOTH-DEPTHnr_LoContrastAVG_StdDev_3D-
Variability.73730.surface_shape
These are from a much larger data set
Reza,
There are several options to deal with your issue.
1) The easiest is probably to reverse the polarity of one of the
datasets (metric file columns) using Attributes: Metric: Metric File
Mathematical Operations: Multiply Column A by scalar. Choose the
relevant column, multiply by -1,
Mark,
Donna Hanlon is out for a while - she sent an earlier email heads-up
that she was expecting a baby this month. As of yesterday she has
transited from expectation to reality, with a healthy baby girl.
I have consulted with John Harwell regarding your query.
Unfortunately, we do not ha
Mark,
1. Scenario #1:
A single FMRI scan session, once analyzed, gives me a statistical
volume and an anatomical volume. AFNI automatically knows how to
position the statistical volume so that it is in alignment with the
anatomical volume (by reading the position information from the raw
da
Mark,
I can answer all but one of your questions; John Harwell can chime in
on the remaining question.
David
On Monday, September 29, 2003, at 11:30 PM, Mark A. Pinsk wrote:
Hello, I'm attempting to flatten a left hemisphere monkey surface
with Caret v4.6, created with SureFit. I've gon
Mark,
On looking at the data set you uploaded, it turns out that the
Macaque.TEMPLATE-CUTS.LEFT-HEM.SPHERE.border file you were using was
inadvertently aligned incorrectly, and that was causing the problem you
encountered.
A corrected version has been generated and put into SuMS. It is
ren
On Thursday, October 2, 2003, at 10:26 AM, Carsten Poppinga wrote:
hi,
i've got a small question concerning surefit error correction manually:
how is it possible that i've corrected handles to a total number of
less
than zero?
The handle-counting algorithm implemented in SureFit occasionall
Mark,
The most likely situation is that your fiducial surface is not in
register with the volume and that it needs to be translated by an
appropriate amount. For instance, if your fiducial surface is in the
'native' space for the cropped right hemisphere, and you are looking at
the full brai
Mark,
It won't matter at all which fiducial surface you choose if they
differ only in translation. If they differ in shape (as occurs for
different versions of the human atlas), it would make a very small
difference in the registration, as the fiducial surface is used to
limit areal distort
Mark,
Yes, there is a noticeable asymmetry; I'd call it modest, but that's
clearly in the eye of the beholder.
If you look at a posterior view of the fiducial surface with the
Cartesian Standard cut topology, you can see that the opercular cuts
aren't positioned with perfect symmetry.
You'
The answer to the question is yes. Use the Map fMRI to Surface option
in Caret, as described on p. 36 of Tutorial 1, to generate metric files
for the human colin left and/or right hemispheres (plus the cerebellum
if it is of interest).
DVE
On Tuesday, October 21, 2003, at 04:40 PM, Mark A. P
sets, or if you have
questions/suggestions for John Harwell or myself. If you have
colleagues who might be interested in an introduction to Caret and the
atlases, please forward this email to them.
David Van Essen, John Harwell
Hi Carsten,
Donna's analysis and suggestions were right on the mark. We (and other
labs as well) have successfully registered many partial flat maps to
our atlas.
The main additional clarification arises if your flat map contains
experimental data near a cut that differs from the cuts used
Mark,
I think that there are two possible explanations to what you are
experiencing in this particular case. Both are very plausible based
on my experience.
1) In some hemispheres, shallow cuts into opercular cortex are as good
as deep cuts across the entire operculum in terms of reduci
Mark,
It is indeed a good idea to leave out the CCantToPOS landmark border on
both the individual and the atlas. If you have good cingulate
landmarks, the registration should be fine in this region.
David
On Jan 8, 2004, at 6:26 PM, Mark A. Pinsk wrote:
David recommended that I do the s
Mark,
No, I don't think you're doing anything wrong on your end. Aberrant
border points have cropped up before during registration; in some cases
it seems to be related to points in or near cuts in one of the
surfaces. We've been chipping away at figuring out how to minimize
these irritants
Mark,
Based on the one (fiducial) surface that I was able to view, my
suggestions are as follows.
You want to do the main round of flattening on a surface that has the
'occipital gyrus' (occipital operculum in my terminology, I think)
disconnected (i.e., a 'topo' file with OG nodes disconnec
Rishi,
I'm not sure how to do spherical registration with a partial
hemisphere.
You might have to do flat-based registration. I do recall someone on
the
caret-users list saying they've done spherical registration with
partial
hemispheres, but I'm not sure how this is done. I'm copying David
fully these tips will work straightforwardly for you. If not, you
could try uploading some exemplar data to our website and we can take a
look at the specific problem(s) you are encountering.
David Van Essen
On Apr 1, 2004, at 9:02 AM, John Harwell wrote:
On Wednesday, March 31, 2004, at
Sandra,
Original Message
Subject:caret 4.6 -tutorial 9 question
Date: Fri, 2 Apr 2004 11:49:05 -0800 (PST)
From: Sandra Basic <[EMAIL PROTECTED]>
To: Donna Hanlon <[EMAIL PROTECTED]>
Hi Donna,
It appears that to reconstruct a surface from closely spaced sectio
Veronica,
On Apr 4, 2004, at 8:29 PM, Veronica S. Smith wrote:
When I complete flattening my left hemisphere in Caret 4.6 I want to
orient the surface. However, this is difficult given that I can't
select the tips of the central sulcus on the flat or spherical map
using my own eye and the Ide
Veronica,
It sounds like you may have opened Caret with a cut topo file and not a
closed one, which would have caused it to complain. Be sure you only
select the initial closed topo file. It may even be advisable to
remove any newly made files from the spec file listing (using the 'X'
butto
Sophie,
How does the average and deviation options work? My average map looks
plausible, but my deviation map looks almost identical so i am not
sure if I am misunderstanding it.
Depending on the nature of the data, it may well be that the deviation
is roughly proportional to the average,
Riadh,
As further clarification:
1) Our current human atlas (colin) includes identified sulci, but no
gyral identification yet. (Gyral identification on surface
reconstructions exist on our older 'Visible Man' atlas - Van Essen &
Drury, J Neurosci 1997 - and will eventually be added to the c
Mark,
DAVID or JOHN H: Although this is an occipital lobe, the cut face is
further anterior than the demo volume, so there still is a substantial
chunk of medial wall left (see calcarine.jpg below). Would
you also cut along the medial wall, as well, in this case?
I would be sure that the fi
AM CDT
To: David Van Essen <[EMAIL PROTECTED]>
Cc: Patrick De Maziere <[EMAIL PROTECTED]>, Donna Hanlon
<[EMAIL PROTECTED]>
Subject: Re: Parameter adjustments for spherical registration
Hi Patrick,
This only pertains if you are using version 5.1 or later.
If you create a set o
Another partial work-around is to reduce the node size (D/C: Surface
Miscellaneous: Node Size) to its current minimum of 1 mm instead of the
default of 2. This won't eliminate the node (unless/until John allows
this to be set to 0) but it does make the nodes much less obtrusive.
DVE
On J
Ed,
Donna's comments are (as usual) on the mark. I have several additional
questions/comments.
1) What cortical layer do your contours represent? I'm guessing from
your figure that they represent the pial surface, or something close to
it. In that case, there is an inherent problem, be
Johannes,
Hopefully, Donna's instructions worked for your immediate purposes.
Depending on your specific purpose, there are other options for showing
the nature and magnitude of the spherical deformations, using the
original sphere and the deformed sphere (but with the same node number
as the
sis options that are not currently
available in Caret, we are receptive to suggestions that would be
useful to multiple investigators.
David Van Essen
On Jul 13, 2005, at 9:13 AM, Donna Hanlon wrote:
Sorry -- I should have mentioned that you can save the resulting
surface_shape file in A
Brige,
The SureFit segmentation algorithm was originally designed for
segmenting T1-weighted MRI's of human cerebral cortex, plus other
volume data that have similar shape and image intensity attributes.
The fundamental requirements are that cortical gray matter be about 3
voxels thick and t
Joe,
If you're doing spherical registration to the PALS atlas, then the
bordercolor file you want should be the following one that can be
downloaded from SumsDB:
ForSPHERICAL.REGISTRATION_Human.Class3.bordercolor
http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=5993911
If that d
Joe,
You can have many topo files loaded at one time, and each coord file
can be associated with its own topo file. If things don't look right,
then use Surface: Topology: Assign Topology to Surface to make sure you
have the desired matchup (e.g., cut topo for FLAT map). I'm guessing
th
Terry,
On Sep 3, 2005, at 6:07 PM, Terry Sewards wrote:
Hi,
Is there a way in which areas can be removed from a *.paint file
without converting the binary file to text and manually deleting the
entries?
Yes. There are two distinct options to choose from.
1) Based on border-drawing.
View
Hi Jochen,
On Oct 13, 2005, at 4:58 PM, Jochen Ditterich wrote:
Hi Donna and John,
I was running into a strange observation when using the "Surface
Outline" function in Caret's MRI viewer. When applying it to your
macaque cortex datasets there seems to be a relatively substantial
misalign
las framework.
Feedback from the user community helps us prioritize what aspects are
most useful to concentrate on.
David
David Van Essen wrote:
Hi Jochen,
On Oct 13, 2005, at 4:58 PM, Jochen Ditterich wrote:
Hi Donna and John,
I was running into a strange observation when using
Hi Jochen,
On Oct 13, 2005, at 4:58 PM, Jochen Ditterich wrote:
Hi Donna and John,
I was running into a strange observation when using the "Surface
Outline" function in Caret's MRI viewer. When applying it to your
macaque cortex datasets there seems to be a relatively substantial
misalign
gram
(314) 747-3073
--
--
*From:* David Van Essen [mailto:[EMAIL PROTECTED]
*Sent:* Friday, October 21, 2005 9:36 PM
*To:* Mike Fox
*Cc:* Donna Hanlon; David Van Essen
*Subject:* Re: visualization specs; MFM vs AFM
Mike,
On Oct 21, 200
On Oct 28, 2005, at 8:03 AM, Donna Hanlon wrote:
Hi all,
For non-human segmenters, .
For the record, this actually refers to human segmenters of nonhuman
brains. We are hoping that Caret segmentation soon becomes
sufficiently automated that chimpanzees can handle it, but we're not
qu
Russ,
I am guessing (hoping) that your query is addressed mainly at the
distinction between 'Average Fiducial Mapping (AFM)' vs.
'Multi-Fiducial Mapping (MFM)', which are the two prime approaches we
currently recommend for mapping to the PALS atlas. If so, I posted a
response to Mike Fox las
Rishi,
There is no generic 'best answer', and the choice of cuts depends on
multiple factors, some related to visualization and others related to
options for subsequent registration to an atlas.
The first question is whether you need to make any cut at all. That
depends on how large your fr
Ed,
Donna's suggestion is in the right direction, but there may be a
problem that entails a bit of extra 'neurosurgery'.
When you use border drawing to reassign paint column data on a 3D
surface, the reassignment currently occurs not only on the nearest
nodes but also on distant nodes that a
ly onto the corresponding fiducial
surface, then combine the foci projection files into a composite.
These will show relative positions on the PALS surface (e.g., the
inflated PALS), but the 3D coordinates will depend on which aveage
fiducial surface is chosen.
Let us know if there are additio
should be concerned.
Thanks,
Leon
Dr. Leon Y Deouell, MD, PhD
Department of Psychology
The Hebrew University of Jerusalem
Jerusalem 91905
Israel
Tel: +972-2-5881739
Fax: +972-2-5825659
http://pissaro.soc.huji.ac.il/~leon/Lab
From: John Harwell <[EMAIL PROTECTED]>
Date: June 7, 2007 3
Antonio et al.,
As Donna's email noted, we have substantially revamped the process of
mapping stereotaxic foci onto the PALS atlas. The revised mapping
methods are best accessed at
http://sumsdb.wustl.edu/sums/stereotaxictocaretfoci.do
or, equivalently, from:
Tutorials: Converting
Stereotax
Brian,
Your question gets at the heart of the differences between AFM
(average fiducial mapping) and MFM (multi-fiducial mapping), which is
discussed in my 2005 Neuroimage paper.
In essence, the MFM value at a given node is the average of the value
for the corresponding nodes in the 12 fi
Alex, Stephanie, et al.,
1) Stephanie's RGB suggestion provides one excellent option for you
to check out.
2) Another set of options is to use the Surface: ROI window, which
allows you flexibility in selecting various regions using data in a
metric column. Then use the Surface ROI: Opera
Hamied,
Donna is correct that Romanski et al is not one in our F99 atlas
dataset.
There are various other schemes that include auditory cortex and are
available on our macaque F99 atlas
(see Macaque.F99.RIGHT.DEMO.73730.spec in
http://sumsdb.wustl.edu/sums/directory.do?
id=6585200&dir_nam
Hi again Hamied,
One minor clarification regarding the thickness. Since the macaque
cortex is only ~1.5 mm thick, you should modify the default settings
to a smaller value. Good results come from a choice of +/- 0.75 mm,
though you can fine tune that if you are doing detailed quantitative
Christa-Lynn,
Two comments.
1) Working from the menu options, you can use the Surface: Region of
Interest window to do something that I think is close to what you want.
Select your overall ROI. If, for example, you want everything except
the medial wall, choose
Selection Method: Nodes wi
Jessica,
On Jan 20, 2008, at 7:18 PM, jessica f cantlon wrote:
I have a beginner's question about using caret to project foci to
the PALS atlas. When I go to do that I get the message "These foci
do not have associated stereotaxic spaces:" and it lists all of
them, even though I have gone
Jessica,
Answers to both questions:
On Jan 21, 2008, at 10:04 AM, jessica f cantlon wrote:
Thank you David...I started over and everything looks to be working
now.
Good!
I was wondering if there is any info about how to estimate peaks as
spheres and then flatten them. I saw an article t
Sofia,
The link you showed worked for me this morning, so I am puzzled as to
why you had a problem. Try the following link instead:
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6588227
It is identical to the one you used except that it doesn't include the
':8081' port, and it rep
ci colors. If you have a small number of classes, this may
be easier, and in any event it allows for post hoc adjustment of the
colors.
David
thanks,
jessica
David Van Essen wrote:
Jessica,
Answers to both questions:
On Jan 21, 2008, at 10:04 AM, jessica f cantlon wrote:
Thank you Davi
Amy et al.,
As it happens, I was having what appears to be the same problem when
attempting to map a functional volume myself yesterday and today! It
seems to be a glitch in Caret that occurs ONLY when you de-select
everything except 'Show mapping to average fiducial surface'.
Try leavin
Krishna,
Caret's segmentation algorithm was originally generated for humans and
has not yet been fully customized for the macaque. However, i would
not expect the behavior you describe.
Try uploading your dataset to
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
Then let Donna Dierker ([EMA
Alex,
You can go to
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6660535&archive_name=Macaque.F99.RIGHT.DEMO.73730.spec
and launch WebCaret (by clicking on the brain icon).
The pulldown 'Scenes' menu lists a set of 20 scenes that can be
selected for viewing. Scene 9 shows in Window
Paul,
On Mar 10, 2008, at 5:04 PM, Paul Rasser wrote:
Could you please let me know why Brodmann's areas 12 and 34 were not
included in the subdivision of the Human.colin atlas?
Thanks,
Paul Rasser
Area 34 is in the medial hippocampal region (just anterior and medial
to area 28) and is n
Rishi,
John's matrix-related comments appear to be on track, based on my
superficial reading. But I wanted in particular to follow up on his
comment about future support for Caret-AFNI communication.
We set this up quite a few years ago when Caret didn't handle volume
visualization.
Ca
Antoine et al.,
John's comments are on the mark.
Subdividing cortex into different functional modalities is challenging
to do in macaques, where there is a lot of experimental data, and even
more difficult in humans. Nonetheless, because the issue is of
obvious importance, I stuck my neck
Leeland,
You can get translucency by converting to a vtk model using the Save
option for the Caret coordinate file. This can also preserve surface
coloration. I don't have a lot of experience with this, but John may
be able to provide additional tips now that he is back from Australia.
or may not find it
satisfactory.
David VE
On Jun 29, 2008, at 10:18 PM, David Van Essen wrote:
Leeland,
You can get translucency by converting to a vtk model using the Save
option for the Caret coordinate file. This can also preserve surface
coloration. I don't have a lot of experience
To all,
In case it is useful to anyone following this email thread, the
macaque F6 segmentation volumes (in *.nii format, plus the standard-
mesh surfaces) have now been uploaded to SumsDB and made publicly
available in the following archive:
http://sumsdb.wustl.edu/sums/archivelist.do?arch
Joe,
I don't know if you saw John Harwell's follow-up email, appended
below, suggesting that Manish's problem was with an older version of
OSX. Since yours is more recent, there is evidently a different
problem. Unless other users have experienced this and found a
solution, this will ha
Amit,
The answer to your question does depend a lot on whether you need the
left and right hemisphere surfaces truly side-by-side in the same
Caret window. If that is the case, then the links Donna pointed to
are the preferred way to go.
However, for many purposes, it is advantageous to
Andrew,
To amplify on what Donna said about the Caret process.
The closest that Caret software and atlases come to providing uniform
resampling is through the use of our 'standard-mesh', 73,730-node
spherical mesh:
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6362810&archive_name
Terry,
1) Donna's suggestion from earlier today is a good one and should work
for your situation.
2) In addition, I have tracked down and fixed the problem with the
missing left hemisphere deformation-map file in question. It was
somehow inadvertently left out of the archive that was upl
Terry,
Several comments.
On Sep 17, 2008, at 5:53 PM, Terry wrote:
Hi,
I'm now trying to deform some borderproj files from the Macaque F99UA1
atlas to the Colin atlas. I first obtained a deform_map file by
applying a spherical deformation, using a particular set of landmarks.
Then, when I tr
Hi Alireza,
One more option to add to Donna's good summary.
You can use Attributes: Metric: Convert Metric to RGB Paint. This
brings up a reasonably self-explanatory popup window that allows you
to assign one metric columns to the 'R' channel, another to the 'G'
channel, and a third to t
Alireza,
To expand on what Donna said,
The foci and foci projection (fociproj) file types in Caret are likely
to be useful for the needs that you describe. For example, if you
enter the center of your ROI as a stereotaxic focus in an identified
stereotaxic space, you can then project it to
Bela,
Donna's comments are on the mark. Two additional points:
1) As you evaluate landmarks, use the 'Show First Link Red' option to
make sure that landmarks are not only in a reasonable location
relative to other landmarks but also are oriented consistently in the
source and target surfac
Yune,
On Mar 17, 2009, at 9:36 AM, life1...@gmail.com wrote:
> Dear Caret users,
>
> I'm a newbie for caret and just started following the tutorial for
> online caret.
> I didn't seem to find MFM –BURTON_04_VibroTactile SIGHTED in Metric
> of D/C and wonder if this tutorial is out-of-date.
T
Alex,
Layers>Foci>Edit Foci Colors is one option for generating colors, but
it is indeed tedious if you have more than a few to assign.
A better way is to capitalize on a color-creation option that John
recently implemented in Window -> Caret Command Executor.
Select COLOR FILE CREATE MISSING
Jinhui,
The 73730-node (standard-mesh) colin surfaces are accessible in
SumsDB. If you want just the coordinate files, select:
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6154943
(archive_name=Human.colin.R.RegToPALS_B12.LR.FIDUCIAL.TLRC.711-2B.
71723.coord)
http://sumsdb.wustl.e
nd you suggested but got the
> following error
>
> COMMAND FAILED
>
> ERROR: Unrecognized operation:
> -color-file-create-missing-colors
>
> Not sure if this is because I might not have correctly-projected foci.
>
> Thanks again for your help,
> Alex
>
>
> On
ather than class (?)
>
> On 01/04/2009 14:00, "David Van Essen"
> wrote:
>
>> Alex,
>>
>> 1) Did you turn on the foci view in Display Control -> Foci Main?
>>
>> 2) What version of Caret are you using? I think it needs to be Caret
>> 5
Yune,
I suggest you read the following for an explanation.
On navigating the human cerebral cortex: response to 'in praise of
tedious anatomy'.
Van Essen DC, Dierker D.
Neuroimage. 2007 Oct 1;37(4):1050-4; discussion 1066-8. Epub 2007 Sep 4.
PMID: 17766148
David
On Apr 7, 2009, at 8:26 AM, Y
YSL,
Most of the foci at issue are in the cerebellum, which is not in view
in your main window. If you project all foci to the 'PC-CC' (PALS-
Cerebral, Colin-Cerebellar) atlas, then you will be able to see the
cerebellar foci in relation to the cerebellar cortical surface.
One focus does ap
YSL,
Basically, '???' means that there was no specific assignment for that
node in that column of the paint file. Use Display Control: Page
Selection: Paint Selection to see what was mapped for that particular
column (e.g., the 4th column is probably visuotopic areas, which only
cover a
Dr. Wang,
Donna's suggestions are good ones. Two other possibilities spring to
mind.
1) Are you looking at the results of multi-fiducial mapping (chosen in
the 'mapping atlas' window once you have selected the PALS_B12 atlas
left or right hemiephere)? This gives substantially different re
Traci,
An addendum (actually an intercalation) to John's suggestion:
On Jun 11, 2009, at 11:33 AM, John Harwell wrote:
> Traci,
>
> Select Attributes Menu->Paint->Assign Paint Names and Properties.
>
Select the appropriate column in the Column Selection pulldown. This
is a nice feature that l
Marc,
Matt's analysis is correct. But if you have multiple topo files
loaded, use the Surfaces: Topology: Set Topology Assigned to Surfaces,
select the flat coord file, and assign it to the the desired cut
topo. Once duly assigned, then save the flat coord file (overwriting
the old versi
I think you mean "could maintain node correspondence when switching
>> between F6 and F99 surfaces in the same .spec file," based on my
>> understanding of your previous paragraph.
>>
>> Again, I can't explain what you saw in the paragraph preceding my
>
proper use of
these datasets and mapping algorithms. Ideally, these would be
covered in a specific tutorial, but we won't have a chance to generate
that for a while.
I hope this helps.
David
From: David Van Essen
Date: May 27, 2009 10:59:12 PM CDT
To: Brad Dickerson
Cc: Donna Dier
Alex,
If the partial hemisphere originated from a SureFit-based segmentation, then
the preferred solution would be to capitalize on an existing process for
extending the cut face portion of the segmentation.
In your case, it looks like you used a different method for generating the
surface,
Jidan,
Here are additions to Donna's comments.
On Dec 28, 2009, at 8:22 AM, Donna Dierker wrote:
> That is way too hard of a question on the Monday morning following a
> long weekend. ;-)
Agreed - but your questions raise important issues. See further inline comments
>
> On 12/28/2009 02:55 AM,
1 - 100 of 139 matches
Mail list logo
