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Today's Topics:
1. Caret for ERP study (Wichian Sittiprapaporn)
2. Re: Caret for ERP study (Morgan Hough)
3. Re: vasculature & segmentation (Johannes Klein)
4. Re: 3d brain and placing foci on T&T coordinates (David Van Essen)
5. Re: Caret for ERP study (David Van Essen)
----------------------------------------------------------------------
Message: 1
Date: Sat, 17 Dec 2005 15:21:05 +0700
From: Wichian Sittiprapaporn <[EMAIL PROTECTED]>
Subject: [caret-users] Caret for ERP study
To: caret-users@brainvis.wustl.edu
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Dear Caret Members,
I have recently installed the Caret program into my lab. Could
anyone let me
know whether the Caret can import the ERP data in order to visulaize
the
brain localization?
With best regards,
--
Wichian Sittiprapaporn, Ph.D.
Electroneurophysiology Laboratory
Neuro-Behavioural Biology Center
Mahidol University, Salaya
Nakhon Pathom 73170
THAILAND
Telephone +(662) 441-9321
Fax +(662) 441-9743
Mobile +(661) 444-0261
Email: [EMAIL PROTECTED]
Email: [EMAIL PROTECTED]
Web: http://neuroscience.mahidol.ac.th
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Message: 2
Date: Sat, 17 Dec 2005 09:43:29 +0000
From: Morgan Hough <[EMAIL PROTECTED]>
Subject: Re: [caret-users] Caret for ERP study
To: "Caret, SureFit, and SuMS software users"
<caret-users@brainvis.wustl.edu>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain
I don't speak for the Caret developers but since morning arrives
earlier
for me I will reply first. I don't know of any source localization
functionality in Caret although once you have data localized you can
then treat it like FMRI data (I am speaking more of distributed
solutions rather than dipole results). There are some open source
packages for doing the localization but most of them do require MATLAB.
You can find links from http://www.fmrib.ox.ac.uk/~mhough/matlab.html.
BrainStorm, EEGLAB, fieldtrip and now spm5 all have some source
localization functionality. It really depends on what you want to
do. Do
you want to do cortically constrained distributed solutions or some
dipole fitting? How many electrodes do you have? BTW, if you don't have
MATLAB you can get fieldtrip to work with octave if you use the version
from the NIMH MEG center (I should add that as a link too really).
Hope this helps.
Cheers,
-Morgan
On Sat, 2005-12-17 at 15:21 +0700, Wichian Sittiprapaporn wrote:
Dear Caret Members,
I have recently installed the Caret program into my lab. Could anyone
let me know whether the Caret can import the ERP data in order to
visulaize the brain localization?
With best regards,
--
Wichian Sittiprapaporn, Ph.D.
Electroneurophysiology Laboratory
Neuro-Behavioural Biology Center
Mahidol University, Salaya
Nakhon Pathom 73170
THAILAND
Telephone +(662) 441-9321
Fax +(662) 441-9743
Mobile +(661) 444-0261
Email: [EMAIL PROTECTED]
Email: [EMAIL PROTECTED]
Web: http://neuroscience.mahidol.ac.th
_______________________________________________
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
------------------------------
Message: 3
Date: Sat, 17 Dec 2005 10:30:05 +0000
From: Johannes Klein <[EMAIL PROTECTED]>
Subject: Re: [caret-users] vasculature & segmentation
To: "Caret, SureFit, and SuMS software users"
<caret-users@brainvis.wustl.edu>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Clayton,
I don't know if this is an option for you - use an MPRAGE sequence
instead of a FLASH, you'll get much less vasculature in your image
volume and better grey/white contrast.
Re tweaking Caret, I'd suggest trying different peaks, have a look at
Donna's peak tweaking tips on the caret web site. I usually have to
skew
my choice a bit to the left.
Cheers,
Johannes
Clayton Curtis schrieb:
I've recently been using Caret to segment brains and have been looking
for ways to reduce the amount of time needed to hand-clean the
topological errors. I've found that using FSL's susan_smooth twice on
an image and correcting for inhomogeneity of signal intensity REALLY
helps tremendously. However, I'm still having to do quite a bit of
hand-cleaning almost entirely due to high intensity (bright white)
voxels of the vasculature confusing the g/w matter algorithm. I'm
writing to ask if anyone has a good solution to this problem. I've
tried to null voxels above a certain cutoff but that appears to grab
too many voxels in true white matter.
Thanks for any suggestions!
*/cc*
*
*
*Clayton E. Curtis, Ph.D.*
*Psychology & Neural Science*
*New York University*
*6 Washington Place, Room 859*
*New York, NY 10003*
*Office - 212.998.3730*
*Lab - 212.998.8347*
*Fax - 212.995.4562*
*http://www.psych.nyu.edu/curtislab*
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------------------------------
Message: 4
Date: Sat, 17 Dec 2005 09:44:01 -0600
From: David Van Essen <[EMAIL PROTECTED]>
Subject: Re: [caret-users] 3d brain and placing foci on T&T
coordinates
To: "Caret, SureFit, and SuMS software users"
<caret-users@brainvis.wustl.edu>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="us-ascii"
Erin,
I hope you found the suggestions from John and Donna to be helpful
(or at least understandable).
Depending on your specific needs, there is another strategy that may
prove useful for you. It involves simultaneously loading the left
and right hemispheres for the average PALS fiducial surfaces
(possible because they have identical node numbers), then viewing
each one in a separate Caret window.
I have generated a suitable both-hemisphere PALS dataset, along with
an accompanying scene that gets everything set up for initial
viewing, and uploaded it to SumsDB. It is now publicly available and
can be visualized using WebCaret.
Go to http://sumsdb.wustl.edu/sums/archivelist.do?
archive_id=6436012. Press the 'brain' icon to the left of PALS_AFNI-
TLRC_AvgFIDUCIALS_sMRI.73730.spec to launch WebCaret.
The first (default) scene will show a dorsal view of the average
fiducial (in AFNI-Talairach space). The second scene switches to the
right hemisphere. The 3rd and 4th scenes show the same fiducial
surfaces combined with the average stuctural MRI volume. The 5th
scene shows the left and right hemispheres simultaneously in separate
windows. If you want to see contours of each hemisphere in the
volume slice, you can see one at a time and switch between them using
the 'Surface Miscellaneous: Active Fiducial' pulldown menu in the
Display Control window.
While this strategy won't let you view both hemispheres
simultaneously in a SINGLE window, it has some advantages/convenience
over what John described in the preceding email.
BEWARE, however, that if you start using this strategy routinely for
your analyses, you will very likely discover that special care is
needed to insure that the left and right hemisphere sulcal depth maps
are displayed correctly on the left and right hemisphere surfaces.
The scenes are preconfigured so that you don't have to think about
this. Our tutorials do not yet cover this new, advanced capability,
so if you experience problems let 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 will ever happen. In the meantime the
following procedure should allow you to view a left and right
hemisphere and foci simultaneously.
* Load a left hemisphere into Caret.
* From the file menu, select "Export File". set the File Type to
"VTK Surface File". At the bottom of the dialog, set "Export
Selections" to "Fiducial...". Enter a name like left_hemisphere.vtk
and save the file.
* Quit Caret.
* Load a right hemisphere into Caret.
* Choose Open Data File from the File Menu. Set the File Type to
"VTK Model File". Select and load the VTK file that you saved a
previous step. You should now see both hemispheres.
* Enter/load Foci for both hemispheres.
* Save the foci file using File Menu: Save Data File. On the save
data file dialog set the File Type to "Foci Files (*.foci)" and make
sure the selection "Foci Associated With Surface Type" (at bottom of
Save Data File dialog) is set to Fiducial.
* When you start Caret in the future both the foci and VTK model file
should be listed in your spec file.
----------------------------------------------------------
John Harwell
[EMAIL PROTECTED]
314-362-3467
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Message: 5
Date: Sat, 17 Dec 2005 10:51:51 -0600
From: David Van Essen <[EMAIL PROTECTED]>
Subject: Re: [caret-users] Caret for ERP study
To: "Caret, SureFit, and SuMS software users"
<caret-users@brainvis.wustl.edu>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
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
encourage this, especially since it would be valuable to use our new
PALS human cortical atlas (http://www.ncbi.nlm.nih.gov/entrez/
> query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16172003;
> http://dx.doi.org/10.1016/j.neuroimage.2005.06.058) to bring ERP data
into a common spatial framework with a growing amount of other
neuroimaging data that resides in our Sumsdb database (http://
> sumsdb.wustl.edu/sums/).
As Morgan indicated, if your data are distributed and voxel-based,
then they can be read directly into Caret if they are in standard
volumetric format (e.g., Analyze, AFNI) or can be converted to such.
If you have dipole data, it should be possible to read in the
coordinates as a 'foci' file, with format specifications described in
the Caret Help menu (Files: File formats). Caret currently doesn't
have the capability to show dipole vector orientation, though that
should not be difficult to incorporate as a new feature if there is
general interest.
If neither of these strategies will work for your needs, we will need
to know more about the technical specifics of the problem.
David VE
On Dec 17, 2005, at 3:43 AM, Morgan Hough wrote:
I don't speak for the Caret developers but since morning arrives
earlier
for me I will reply first. I don't know of any source localization
functionality in Caret although once you have data localized you can
then treat it like FMRI data (I am speaking more of distributed
solutions rather than dipole results). There are some open source
packages for doing the localization but most of them do require
MATLAB.
You can find links from http://www.fmrib.ox.ac.uk/~mhough/matlab.html.
BrainStorm, EEGLAB, fieldtrip and now spm5 all have some source
localization functionality. It really depends on what you want to
do. Do
you want to do cortically constrained distributed solutions or some
dipole fitting? How many electrodes do you have? BTW, if you don't
have
MATLAB you can get fieldtrip to work with octave if you use the
version
from the NIMH MEG center (I should add that as a link too really).
Hope this helps.
Cheers,
-Morgan
On Sat, 2005-12-17 at 15:21 +0700, Wichian Sittiprapaporn wrote:
Dear Caret Members,
I have recently installed the Caret program into my lab. Could anyone
let me know whether the Caret can import the ERP data in order to
visulaize the brain localization?
With best regards,
--
Wichian Sittiprapaporn, Ph.D.
Electroneurophysiology Laboratory
Neuro-Behavioural Biology Center
Mahidol University, Salaya
Nakhon Pathom 73170
THAILAND
Telephone +(662) 441-9321
Fax +(662) 441-9743
Mobile +(661) 444-0261
Email: [EMAIL PROTECTED]
Email: [EMAIL PROTECTED]
Web: http://neuroscience.mahidol.ac.th
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