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
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
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
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,
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
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
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.
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 the Surface
Outline
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
: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 relative
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
on fiducial surface (David Van Essen)
---
--
-
Message: 1
Date: Sat, 1 Apr 2006 22:36:15 -0700
From: Terry Sewards [EMAIL PROTECTED]
Subject: [caret-users] Re: Drawing borders on fiducial surface
To: caret-users@brainvis.wustl.edu
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
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
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
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
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
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
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
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:
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
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
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
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 David...I started over and everything looks to be
working now
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
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
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.
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
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.
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
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
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
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
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
Alex,
LayersFociEdit 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
Not sure if this is because I might not have correctly-projected foci.
Thanks again for your help,
Alex
On 01/04/2009 13:03, David Van Essen vanes...@brainvis.wustl.edu
wrote:
Alex,
LayersFociEdit Foci Colors is one option for generating colors, but
it is indeed tedious if you have more
/2009 14:00, David Van Essen vanes...@brainvis.wustl.edu
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
5.61.
If this doesn't solve it, John will need to chime in as I'm off to a
meeting
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,
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
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
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 vanes...@brainvis.wustl.edu
Date: May 27, 2009 10:59:12 PM CDT
To: Brad Dickerson br...@nmr.mgh.harvard.edu
Cc
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,
Jidan,
On Dec 29, 2009, at 6:16 AM, z丹丹 wrote:
Your asumption is right. Here is the analysis I wan t to do. I have a 3D
fiducial surface , based on this fiducial surface ,let's say, template, I
generated some simulated fiducial surface with some deformation, let's say
subject. So
YSL,
Two other options to try:
1) Select the palette PSYCH rather than PSYCH-NO-NONE, which differs only in
how near-zero is handled.
2) Click on a node in the blue patch in question, and use the ID Window to
determine what the actual metric value(s) are for those nodes in the metric
column
Jochen,
Loading the segmentation volume plus the original MR volume should allow you to
select:
Volume: Segmentation: Edit Voxels. This lets you add missing parts to your
heart's content.
David
On Apr 5, 2010, at 4:28 PM, Jochen Ditterich wrote:
Thank you, Donna!
I am apparently
Matt,
I found this previous posting:
http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg00203.html
explaining you should not cross over cortical contours and not jump widely
from one section to the next.
Are these the only issues one should be worried about?
Yes, basically.
Joost,
In addition to Donna's pointers, check out:
Van Essen, D.C., Dierker, D., Snyder, A., Raichle, M.E., Reiss, A., and
Korenberg, J. (2006) Symmetry of cortical folding abnormalities in Williams
syndrome revealed by surface-based analyses. J. Neuroscience 26:5470-5483
It shows how
Tristan,
On Jan 17, 2011, at 6:56 AM, Tristan Chaplin wrote:
Hi,
I'm working on constructing brain models from histological sections with
cortical areas demarcated. Until now we've been writing our own progrms to
achieve this. I'd like to start to use Caret for more of this work so
Yang et al,
A tutorial document and associated dataset for registering Freesurfer macaque
datasets to F99 are available at the following URL:
http://sumsdb.wustl.edu/sums/directory.do?id=8285961dir_name=FREESURFER-to-F99
For future reference, FREESURFER-to-F99 is a subdirectory of the TUTORIALS
Hi Colin,
Regarding (1), we will have a new Caret release this coming week. I'm not sure
whether it's likely to help with your ubuntu problem, but Jon Schindler and/or
Jon Harwell might have a clue.
Regarding (2) you can use Surface: Region of Interest Operations, then select
all nodes;
Also, if you have not yet projected the foci, they will not be visible unless a
'fiducial' surface is displayed in the main window.
David VE
On Feb 16, 2011, at 3:04 PM, Erin Reid wrote:
David,
First check to make sure you have Show Foci checked in the D/C menu: Foci
Main page. If that is
Colin,
Segmentation produces a 'native mesh' whose exact node number cannot be
prespecified in Caret (or in other segmentation algorithms I know about).
The 73,730-node mesh ('74k' in our latest lingo) arises from surface-based
registration to an atlas - either the macaque F99 atlas (a 74k_f99
Tristan,
Registering from a left hem source to a right hem target (or vice versa) should
work for the LVD as well as the LPR algorithm. I've done it myself on multiple
occasions.
Importantly, your source and target spec files must have the correct hemisphere
assignment. Check that
Sam,
It is possible to carry out the conversion you desire in a single step. First,
some clarifying comments.
1) What you call 'Caret 164k mesh' is what we call the '164k_fs_LR' mesh, to
signify that it is derived from registering the fsaverage left hem (164k_fs_L
mesh) and right hem
Colin.,
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8293370archive_name=Macaque.PHT00.R.REGISTER-with-F99.41218.spec
is a newly uploaded archive that contains the PHT00 with its native mesh. The
paint colors are very different from those on the F99 atlas, and there may be
some
Hello Nik,
Here is the solution to the mystery:
The tutorial as it currently runs expects the user to start with the right
hemisphere (stated near bottom of p. 2). The file that you need for stage 1 of
the left hemisphere is created during Stage 3 for the right hemisphere (see
below). This
Pablo,
On a Mac, use 'Shift-click' to complete whatever edits you have started in
border update. (It may be ctrl-click or something else on linux or a PC).
This appiies to the erase, extend, or replace options.
The 'Apply' button is what you need to press in order to get started in the
Pablo,
Registration to F99 should not be impacted by issues of scaling. (For example,
it doesn't affect our monkey-to-human registration despite large scale
differences.) But if you want to rescale just for the sake of veridical
representation, you can use
caret_command
. Re: part of a surface (David Van Essen)
3. Re: Freesurfer Surface and Volume are not in register when
shown in Caret (Pablo Polosecki)
4. Re: Freesurfer Surface and Volume are not in register when
shown in Caret (David Van Essen)
-- Forwarded message
Hello Dale,
If Donna's explanation is correct (as I suspect is the case), you may have
better results using the Conte69 atlas surface that is registered to the FNIRT
MNI152 volume, In general, we are encouraging investigators to migrate to this
atlas for a number of reasons, including the
Tristan,
I have uploaded to SumsDB a file that should be what you want. However, it is
caveat emptor, as I do not have time at the moment to validate it. Please let
me know if it works properly for you.
David VE
Hi Arman,
Use Attributes: Palette: Edit to modify an existing palette (and rename it) or
to generate a completely new palette. If you like it, be sure to save the
palette file, and to include it when saving scenes of datasets you want to
quickly reload.
David
On Dec 18, 2012, at 11:45 AM,
Colin
You can reconstruct contours from any sectioning plane into a surface. But I
believe the z axis will be that between sections, so you will need to rotate
appropriately at the end.
A white matter surface sill be fine as long as the topology doesn't get messed
up by thin gyral blades.
Shahin et al.,
In the SumsDB database you can go to
http://sumsdb.wustl.edu/sums/directory.do?id=8291757dir_name=Inter-atlas_deformation_maps
and download
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8293223archive_name=inter-atlas_deformation_maps.zip
The
To all,
I think the key distinction may be whether the 'foreground' and 'background'
surfaces are on opposite sides of the origin. (John Harwell can correct me if
I'm wrong.) A surface can be translated so that its center of gravity is at
the origin in order to achieve that end.
David
On
Hello Milan,
Years ago, I generated the Brodmann surface-based maps in Caret by manually
estimating areal boundaries on a surface-based atlas using as a reference the
classical Brodmann drawing of a right hemisphere (reprinted in Polyak, 1947).
Because this illustration did not include
Alternatively, you may find that FreeSurfer will work better for your current
needs. Matt Glasser and others have gotten it to work reasonably well on
macaque structural images.
David
On Oct 15, 2014, at 2:38 AM, Donna Dierker do...@brainvis.wustl.edu wrote:
Hi Aditya,
On monkeys, yes.
and existing users of HCP data, methods, and
tools, and will cover both basic and advanced topics.
Faculty listings and the full schedule of covered topics, more info, and
register on the HCP Course website. We hope to see you in Hawaii!
Best,
2015 HCP Course Organizers
David Van Essen, Jenn Elam
/zip_targz_tgzCARET.QUICK-START.03-06.tar.gz/568256_info.html
but the correct URL can be achieved by inserting a single ‘/‘ between ‘tgz’
and 'CARET’ :
http://brainvis.wustl.edu/sumsdb/zip_targz_tgz/CARET.QUICK-START.03-06.tar.gz/568256_info.html
> On Feb 7, 2017, at 6:47 PM, David Van Essen <
To all,
1) For mapping FreeSurfer data to ‘fs_LR’ (Conte69) space we now recommend
using a streamlined process described in:
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?
and the Resampling-FreeSurfer-HCP.pdf
e CARET_TUTORIAL_SEPT06.zip dataset at
> http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595030
> <http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595030>
> Could I download the dataset from other link?
> Thank you!
>
> Muchen
On Feb 7, 2017, at 6:47 PM, Dav
Hi Tony et al.
John’s explanation regarding deformation map files is correct. Here, I’m
drawing to your attention the fact that Connectome Workbench (and wb_command)
provides improved methods for mapping from one surface mesh that has been
registered to another (see below). Depending on your
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