Re: [caret-users] help mapping an SPM5 activation volume to a surface

[David Van Essen]

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 view the left and  
right hemispheres in separate Caret windows (sized identically, and  
sometimes with the left and right hemisphere views yoked together).   
To do this, it is easiest to start with an existing dataset that has  
the relevant files loaded and display features conveniently set up.   
More specifically, go to:  http://sumsdb.wustl.edu/sums/humanpalsmore.do

In the PALS_B12.BOTH-HEMS.STANDARD-SCENES
row, select 'View Online (WebCaret) if you want a quick look at what's  
in the dataset, and choose 'Go to Data Directory' if you want to  
download it.

http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595788&archive_name=PALS_B12.BOTH-HEMS.STANDARD-SCENES.73730.spec
is an archive that has standard scenes for both hemispheres.

Importantly, this setup allows data that differ for the left and right  
hemisphere to be assigned separately to each surface.  This capability  
is powerful and flexible, but you do have to be careful that what you  
see displayed is in fact what you want.


If you find an alternate set of surface configurations and data  
assignments works better for you as a starting point, be sure to save  
it as a scene so that you can use it as your own customized starting  
point in the future.


David VE

On Aug 6, 2008, at 7:54 AM, Donna Dierker wrote:


Hi Amit,

Please see these recent caret-users posts on the same topic:

http://brainvis.wustl.edu/pipermail/caret-users/2008-July/001468.html
http://brainvis.wustl.edu/pipermail/caret-users/2008-July/001470.html

Donna

On 08/06/2008 02:06 AM, Amit Etkin wrote:

Hi Donna,

Thank you for the prompt reply and the link to the data. So far I'm
making good progress on my mapping of functional to surface, but have
a question in the process...is it possible to display the right and
left hemispheres side by side (positioned correctly) at the same  
time?


thanks,

Amit

On Tue, Aug 5, 2008 at 6:38 AM, Donna Dierker
<[EMAIL PROTECTED] > wrote:

   Hi Amit,

   See inline replies below.

   Donna

   On 08/05/2008 01:20 AM, Amit Etkin wrote:

Hi all,

I'm trying to map my activation map (spm_T's written out as .img and
.hdr pairs) from SPM5 onto a surface in Caret, and getting more
confused the more I do. I've gone through the tutorial, can map
activation files and can even get my activation file mapped, but

   have

a number of questions about how I should go about doing that below:

   As far as I know, Caret still can't read .img/.hdr NIfTI pairs, so
   write
   your spm_T's out in .nii form for feeding to Caret.


1. Which spec file should I use? If I want to do the MFM approach,
then it seems I need to select the Human.PALS_B12.LR.MULTI-
FIDUCIAL_SPM2_fMRI-MAPPER.B1-12.LEFT.73730 file, for example, but it
doesn't seem to have surface with the 12 subjects averaged. If I

   want

to get the averaged surface, in which case I can only do AFM
registration, I can chose
Human.PALS_B12.LR.AVERAGE-FIDUCIAL_SPM96.LEFT.73730, but then

   can't do

MFM. I'd like to be able to do MFM but display it on the averaged
surface...is that possible? If so, how?

   When I select the SPM2 space and select
   Human.PALS_B12.LR.MULTI-FIDUCIAL_SPM2_fMRI-MAPPER.B1-12.LEFT. 
73730, I

   get a window like the attached capture.  Note that there is a
   distinction between the surface used for mapping and the surface  
used
   for display.  Using the default selections in the attached  
capture,
   Caret will map not only to the average SPM2 left surface, but  
also to

   each of the contributing PALS left hems in SPM2 space, and then
   average
   the resulting 12 individual maps.

   Either of these maps (your_vol_on_AFM or your_vol_on_MFM) can be
   displayed on the SPM2 average fiducial surface.  But we usually  
don't
   display fMRI results on average fiducial surfaces.  We usually  
use the

   inflated, sometimes very inflated (for opercular results) or flat
   surfaces.  We do use average fiducial surfaces generated for
   study-specific purposes (e.g., to illustrate morphometric
   differences).
   But it can be a little misleading to display results the PALS  
average
   fiducial, because the audience might be tempted to make the  
implicit
   assumption that your subjects' anatomical features exactly match  
PALS.

   While on a broad level this will be true, on a micro level it
   won't be.


2. When I open a spec file it asks for the space...should I pick

   what

it defaults to or change it to SPM5?

   This reminds me:  Tim Coalson has generated SPM5 surfaces which we
   need
   to package and release.  The only loose end is the cerebellar  
surface.
   I must coordinate with David (and possibly Joern Diedricksen) 

Re: [caret-users] help mapping an SPM5 activation volume to a surface

[Donna Dierker]

Hi Amit,

Please see these recent caret-users posts on the same topic:

http://brainvis.wustl.edu/pipermail/caret-users/2008-July/001468.html
http://brainvis.wustl.edu/pipermail/caret-users/2008-July/001470.html

Donna

On 08/06/2008 02:06 AM, Amit Etkin wrote:

Hi Donna,

Thank you for the prompt reply and the link to the data. So far I'm 
making good progress on my mapping of functional to surface, but have 
a question in the process...is it possible to display the right and 
left hemispheres side by side (positioned correctly) at the same time?


thanks,

Amit

On Tue, Aug 5, 2008 at 6:38 AM, Donna Dierker 
<[EMAIL PROTECTED] > wrote:


Hi Amit,

See inline replies below.

Donna

On 08/05/2008 01:20 AM, Amit Etkin wrote:
> Hi all,
>
> I'm trying to map my activation map (spm_T's written out as .img and
> .hdr pairs) from SPM5 onto a surface in Caret, and getting more
> confused the more I do. I've gone through the tutorial, can map
> activation files and can even get my activation file mapped, but
have
> a number of questions about how I should go about doing that below:
As far as I know, Caret still can't read .img/.hdr NIfTI pairs, so
write
your spm_T's out in .nii form for feeding to Caret.
>
> 1. Which spec file should I use? If I want to do the MFM approach,
> then it seems I need to select the Human.PALS_B12.LR.MULTI-
> FIDUCIAL_SPM2_fMRI-MAPPER.B1-12.LEFT.73730 file, for example, but it
> doesn't seem to have surface with the 12 subjects averaged. If I
want
> to get the averaged surface, in which case I can only do AFM
> registration, I can chose
> Human.PALS_B12.LR.AVERAGE-FIDUCIAL_SPM96.LEFT.73730, but then
can't do
> MFM. I'd like to be able to do MFM but display it on the averaged
> surface...is that possible? If so, how?
When I select the SPM2 space and select
Human.PALS_B12.LR.MULTI-FIDUCIAL_SPM2_fMRI-MAPPER.B1-12.LEFT.73730, I
get a window like the attached capture.  Note that there is a
distinction between the surface used for mapping and the surface used
for display.  Using the default selections in the attached capture,
Caret will map not only to the average SPM2 left surface, but also to
each of the contributing PALS left hems in SPM2 space, and then
average
the resulting 12 individual maps.

Either of these maps (your_vol_on_AFM or your_vol_on_MFM) can be
displayed on the SPM2 average fiducial surface.  But we usually don't
display fMRI results on average fiducial surfaces.  We usually use the
inflated, sometimes very inflated (for opercular results) or flat
surfaces.  We do use average fiducial surfaces generated for
study-specific purposes (e.g., to illustrate morphometric
differences).
But it can be a little misleading to display results the PALS average
fiducial, because the audience might be tempted to make the implicit
assumption that your subjects' anatomical features exactly match PALS.
While on a broad level this will be true, on a micro level it
won't be.
>
> 2. When I open a spec file it asks for the space...should I pick
what
> it defaults to or change it to SPM5?
This reminds me:  Tim Coalson has generated SPM5 surfaces which we
need
to package and release.  The only loose end is the cerebellar surface.
I must coordinate with David (and possibly Joern Diedricksen) on that.
Yes, Jay Hegde, I did not forget you; SPM5 surfaces are on the way
VERY
SOON.

For now, select SPM2 (the closest space).
>
> 3. When I map functional volumes to surfaces, I'm only given the
> option of selecting between .hdr not .img files, and then get the
> warning: "You have selected a ".hdr" file. If this ".hdr" file does
> not contain an SPM originator, it is unlikely that it will get
mapped
> to the surface correctly". What does this error mean, and how do I
> know if the hdr contains an SPM originator?
Use SPM5 to write your spm_T's as .nii to resolve this problem.
>
> 4. Do I need to flip along the X axis or change the location of the
> origin of my functional images? If so, how?
If you write as .nii, Caret will flip as needed.
>
> 5. Where do I get flat maps, inflated surfaces and brodman area maps
> like there are in the tutorial?
Here is the Sept 2006 tutorial dataset:

http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595030

Here is the Sept 2006 tutorial document:

http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379

Click on the diskette shaped icon to download them.

Don't be intimidated by the size of the tutorial; skip to Part 5,
section 5.1.
>
> that's all the questions I have for now, and would GREATLY
appreciate
> all the help I can get.
>
> many thanks,
> Amit
>
>
> --

Re: [caret-users] help mapping an SPM5 activation volume to a surface

[Amit Etkin]

Hi Donna,

Thank you for the prompt reply and the link to the data. So far I'm making
good progress on my mapping of functional to surface, but have a question in
the process...is it possible to display the right and left hemispheres side
by side (positioned correctly) at the same time?

thanks,

Amit

On Tue, Aug 5, 2008 at 6:38 AM, Donna Dierker <[EMAIL PROTECTED]>wrote:

> Hi Amit,
>
> See inline replies below.
>
> Donna
>
> On 08/05/2008 01:20 AM, Amit Etkin wrote:
> > Hi all,
> >
> > I'm trying to map my activation map (spm_T's written out as .img and
> > .hdr pairs) from SPM5 onto a surface in Caret, and getting more
> > confused the more I do. I've gone through the tutorial, can map
> > activation files and can even get my activation file mapped, but have
> > a number of questions about how I should go about doing that below:
> As far as I know, Caret still can't read .img/.hdr NIfTI pairs, so write
> your spm_T's out in .nii form for feeding to Caret.
> >
> > 1. Which spec file should I use? If I want to do the MFM approach,
> > then it seems I need to select the Human.PALS_B12.LR.MULTI-
> > FIDUCIAL_SPM2_fMRI-MAPPER.B1-12.LEFT.73730 file, for example, but it
> > doesn't seem to have surface with the 12 subjects averaged. If I want
> > to get the averaged surface, in which case I can only do AFM
> > registration, I can chose
> > Human.PALS_B12.LR.AVERAGE-FIDUCIAL_SPM96.LEFT.73730, but then can't do
> > MFM. I'd like to be able to do MFM but display it on the averaged
> > surface...is that possible? If so, how?
> When I select the SPM2 space and select
> Human.PALS_B12.LR.MULTI-FIDUCIAL_SPM2_fMRI-MAPPER.B1-12.LEFT.73730, I
> get a window like the attached capture.  Note that there is a
> distinction between the surface used for mapping and the surface used
> for display.  Using the default selections in the attached capture,
> Caret will map not only to the average SPM2 left surface, but also to
> each of the contributing PALS left hems in SPM2 space, and then average
> the resulting 12 individual maps.
>
> Either of these maps (your_vol_on_AFM or your_vol_on_MFM) can be
> displayed on the SPM2 average fiducial surface.  But we usually don't
> display fMRI results on average fiducial surfaces.  We usually use the
> inflated, sometimes very inflated (for opercular results) or flat
> surfaces.  We do use average fiducial surfaces generated for
> study-specific purposes (e.g., to illustrate morphometric differences).
> But it can be a little misleading to display results the PALS average
> fiducial, because the audience might be tempted to make the implicit
> assumption that your subjects' anatomical features exactly match PALS.
> While on a broad level this will be true, on a micro level it won't be.
> >
> > 2. When I open a spec file it asks for the space...should I pick what
> > it defaults to or change it to SPM5?
> This reminds me:  Tim Coalson has generated SPM5 surfaces which we need
> to package and release.  The only loose end is the cerebellar surface.
> I must coordinate with David (and possibly Joern Diedricksen) on that.
> Yes, Jay Hegde, I did not forget you; SPM5 surfaces are on the way VERY
> SOON.
>
> For now, select SPM2 (the closest space).
> >
> > 3. When I map functional volumes to surfaces, I'm only given the
> > option of selecting between .hdr not .img files, and then get the
> > warning: "You have selected a ".hdr" file. If this ".hdr" file does
> > not contain an SPM originator, it is unlikely that it will get mapped
> > to the surface correctly". What does this error mean, and how do I
> > know if the hdr contains an SPM originator?
> Use SPM5 to write your spm_T's as .nii to resolve this problem.
> >
> > 4. Do I need to flip along the X axis or change the location of the
> > origin of my functional images? If so, how?
> If you write as .nii, Caret will flip as needed.
> >
> > 5. Where do I get flat maps, inflated surfaces and brodman area maps
> > like there are in the tutorial?
> Here is the Sept 2006 tutorial dataset:
>
> http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595030
>
> Here is the Sept 2006 tutorial document:
>
> http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379
>
> Click on the diskette shaped icon to download them.
>
> Don't be intimidated by the size of the tutorial; skip to Part 5,
> section 5.1.
> >
> > that's all the questions I have for now, and would GREATLY appreciate
> > all the help I can get.
> >
> > many thanks,
> > Amit
> >
> >
> > --
> > Amit Etkin, MD, PhD
> > Department of Psychiatry
> > Stanford University School of Medicine
> > 401 Quarry Road
> > Stanford, CA 94305
> > office: 650-723-2516
> > 
> >
> > ___
> > caret-users mailing list
> > caret-users@brainvis.wustl.edu
> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >
>
> ___
> caret-users mailing list

Re: [caret-users] help mapping an SPM5 activation volume to a surface

[Donna Dierker]

... this time with capture attached.

On 08/05/2008 08:38 AM, Donna Dierker wrote:

Hi Amit,

See inline replies below.

Donna

On 08/05/2008 01:20 AM, Amit Etkin wrote:
  

Hi all,

I'm trying to map my activation map (spm_T's written out as .img and 
.hdr pairs) from SPM5 onto a surface in Caret, and getting more 
confused the more I do. I've gone through the tutorial, can map 
activation files and can even get my activation file mapped, but have 
a number of questions about how I should go about doing that below:

As far as I know, Caret still can't read .img/.hdr NIfTI pairs, so write 
your spm_T's out in .nii form for feeding to Caret.
  
1. Which spec file should I use? If I want to do the MFM approach, 
then it seems I need to select the Human.PALS_B12.LR.MULTI-
FIDUCIAL_SPM2_fMRI-MAPPER.B1-12.LEFT.73730 file, for example, but it 
doesn't seem to have surface with the 12 subjects averaged. If I want 
to get the averaged surface, in which case I can only do AFM 
registration, I can chose 
Human.PALS_B12.LR.AVERAGE-FIDUCIAL_SPM96.LEFT.73730, but then can't do 
MFM. I'd like to be able to do MFM but display it on the averaged 
surface...is that possible? If so, how?

When I select the SPM2 space and select 
Human.PALS_B12.LR.MULTI-FIDUCIAL_SPM2_fMRI-MAPPER.B1-12.LEFT.73730, I 
get a window like the attached capture.  Note that there is a 
distinction between the surface used for mapping and the surface used 
for display.  Using the default selections in the attached capture, 
Caret will map not only to the average SPM2 left surface, but also to 
each of the contributing PALS left hems in SPM2 space, and then average 
the resulting 12 individual maps.


Either of these maps (your_vol_on_AFM or your_vol_on_MFM) can be 
displayed on the SPM2 average fiducial surface.  But we usually don't 
display fMRI results on average fiducial surfaces.  We usually use the 
inflated, sometimes very inflated (for opercular results) or flat 
surfaces.  We do use average fiducial surfaces generated for 
study-specific purposes (e.g., to illustrate morphometric differences).  
But it can be a little misleading to display results the PALS average 
fiducial, because the audience might be tempted to make the implicit 
assumption that your subjects' anatomical features exactly match PALS.  
While on a broad level this will be true, on a micro level it won't be.
  
2. When I open a spec file it asks for the space...should I pick what 
it defaults to or change it to SPM5?

This reminds me:  Tim Coalson has generated SPM5 surfaces which we need 
to package and release.  The only loose end is the cerebellar surface.  
I must coordinate with David (and possibly Joern Diedricksen) on that.  
Yes, Jay Hegde, I did not forget you; SPM5 surfaces are on the way VERY 
SOON.


For now, select SPM2 (the closest space).
  
3. When I map functional volumes to surfaces, I'm only given the 
option of selecting between .hdr not .img files, and then get the 
warning: "You have selected a ".hdr" file. If this ".hdr" file does 
not contain an SPM originator, it is unlikely that it will get mapped 
to the surface correctly". What does this error mean, and how do I 
know if the hdr contains an SPM originator?


Use SPM5 to write your spm_T's as .nii to resolve this problem.
  
4. Do I need to flip along the X axis or change the location of the 
origin of my functional images? If so, how?


If you write as .nii, Caret will flip as needed.
  
5. Where do I get flat maps, inflated surfaces and brodman area maps 
like there are in the tutorial?


Here is the Sept 2006 tutorial dataset:

http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595030

Here is the Sept 2006 tutorial document:

http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379

Click on the diskette shaped icon to download them.

Don't be intimidated by the size of the tutorial; skip to Part 5, 
section 5.1.
  
that's all the questions I have for now, and would GREATLY appreciate 
all the help I can get.


many thanks,
Amit


--
Amit Etkin, MD, PhD
Department of Psychiatry
Stanford University School of Medicine
401 Quarry Road
Stanford, CA 94305
office: 650-723-2516


___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://brainvis.wustl.edu/mailman/listinfo/caret-users
  



___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://brainvis.wustl.edu/mailman/listinfo/caret-users
  


<>

Re: [caret-users] help mapping an SPM5 activation volume to a surface

[Donna Dierker]

Hi Amit,

See inline replies below.

Donna

On 08/05/2008 01:20 AM, Amit Etkin wrote:

Hi all,

I'm trying to map my activation map (spm_T's written out as .img and 
.hdr pairs) from SPM5 onto a surface in Caret, and getting more 
confused the more I do. I've gone through the tutorial, can map 
activation files and can even get my activation file mapped, but have 
a number of questions about how I should go about doing that below:
As far as I know, Caret still can't read .img/.hdr NIfTI pairs, so write 
your spm_T's out in .nii form for feeding to Caret.


1. Which spec file should I use? If I want to do the MFM approach, 
then it seems I need to select the Human.PALS_B12.LR.MULTI-
FIDUCIAL_SPM2_fMRI-MAPPER.B1-12.LEFT.73730 file, for example, but it 
doesn't seem to have surface with the 12 subjects averaged. If I want 
to get the averaged surface, in which case I can only do AFM 
registration, I can chose 
Human.PALS_B12.LR.AVERAGE-FIDUCIAL_SPM96.LEFT.73730, but then can't do 
MFM. I'd like to be able to do MFM but display it on the averaged 
surface...is that possible? If so, how?
When I select the SPM2 space and select 
Human.PALS_B12.LR.MULTI-FIDUCIAL_SPM2_fMRI-MAPPER.B1-12.LEFT.73730, I 
get a window like the attached capture.  Note that there is a 
distinction between the surface used for mapping and the surface used 
for display.  Using the default selections in the attached capture, 
Caret will map not only to the average SPM2 left surface, but also to 
each of the contributing PALS left hems in SPM2 space, and then average 
the resulting 12 individual maps.


Either of these maps (your_vol_on_AFM or your_vol_on_MFM) can be 
displayed on the SPM2 average fiducial surface.  But we usually don't 
display fMRI results on average fiducial surfaces.  We usually use the 
inflated, sometimes very inflated (for opercular results) or flat 
surfaces.  We do use average fiducial surfaces generated for 
study-specific purposes (e.g., to illustrate morphometric differences).  
But it can be a little misleading to display results the PALS average 
fiducial, because the audience might be tempted to make the implicit 
assumption that your subjects' anatomical features exactly match PALS.  
While on a broad level this will be true, on a micro level it won't be.


2. When I open a spec file it asks for the space...should I pick what 
it defaults to or change it to SPM5?
This reminds me:  Tim Coalson has generated SPM5 surfaces which we need 
to package and release.  The only loose end is the cerebellar surface.  
I must coordinate with David (and possibly Joern Diedricksen) on that.  
Yes, Jay Hegde, I did not forget you; SPM5 surfaces are on the way VERY 
SOON.


For now, select SPM2 (the closest space).


3. When I map functional volumes to surfaces, I'm only given the 
option of selecting between .hdr not .img files, and then get the 
warning: "You have selected a ".hdr" file. If this ".hdr" file does 
not contain an SPM originator, it is unlikely that it will get mapped 
to the surface correctly". What does this error mean, and how do I 
know if the hdr contains an SPM originator?

Use SPM5 to write your spm_T's as .nii to resolve this problem.


4. Do I need to flip along the X axis or change the location of the 
origin of my functional images? If so, how?

If you write as .nii, Caret will flip as needed.


5. Where do I get flat maps, inflated surfaces and brodman area maps 
like there are in the tutorial?

Here is the Sept 2006 tutorial dataset:

http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595030

Here is the Sept 2006 tutorial document:

http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379

Click on the diskette shaped icon to download them.

Don't be intimidated by the size of the tutorial; skip to Part 5, 
section 5.1.


that's all the questions I have for now, and would GREATLY appreciate 
all the help I can get.


many thanks,
Amit


--
Amit Etkin, MD, PhD
Department of Psychiatry
Stanford University School of Medicine
401 Quarry Road
Stanford, CA 94305
office: 650-723-2516


___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://brainvis.wustl.edu/mailman/listinfo/caret-users
  

RE: [caret-users] help

[Xu, Ben (NIH/NINDS) [E]]

Yes. I had figured out. 

Thanks.

Ben

-Original Message-
From: John Harwell [mailto:[EMAIL PROTECTED] 
Sent: Thursday, January 11, 2007 4:53 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] help


Hi Ben,

You found an error in the tutorial document.  The statement should  
read "Navigate to the tutorial's top-level directory,  
CARET_TUTORIAL_SEPT06".

Thanks.

--
John Harwell
[EMAIL PROTECTED]
314-362-3467

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.Box 8108
St. Louis, MO 63110   USA

On Jan 11, 2007, at 3:12 PM, Xu, Ben (NIH/NINDS) [E] wrote:

> Hi,
>
>
>
> I'm trying to learn to use CARET. I've installed CARET on my  
> Windows PC and downloaded and unzipped the tutorial data set  
> "CARET_TUTORIAL_Sept06.zip" as instructed in the "Caret Tutorial- 
> the Basics." On page 6 of the manual, it says "Navigate to the  
> tutorial data set's HUMAN_DATA/RIGHT_HEM directory." But, there is  
> no such directory in the extracted file. Did I download a wrong set  
> of data?
>
>
>
> Your help is greatly appreciated.
>
>
>
> Ben
>
> -
>
> Benjamin Xu, Ph.D.
>
> Human Cortical Physiology Section
>
> National Institute of Neurological Disorders and Stroke
>
> National Institutes of Health
>
> 5N234 Bldg 10 Center Dr.
>
> Bethesda, MD 20892-1428
>
> Phone: 301-402-7968
>
>
>
> ___
> caret-users mailing list
> caret-users@brainvis.wustl.edu
> http://pulvinar.wustl.edu/mailman/listinfo/caret-users


___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users

Re: [caret-users] help

[John Harwell]

Hi Ben,

You found an error in the tutorial document.  The statement should  
read "Navigate to the tutorial's top-level directory,  
CARET_TUTORIAL_SEPT06".


Thanks.

--
John Harwell
[EMAIL PROTECTED]
314-362-3467

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.Box 8108
St. Louis, MO 63110   USA

On Jan 11, 2007, at 3:12 PM, Xu, Ben (NIH/NINDS) [E] wrote:


Hi,



I’m trying to learn to use CARET. I’ve installed CARET on my  
Windows PC and downloaded and unzipped the tutorial data set  
“CARET_TUTORIAL_Sept06.zip” as instructed in the “Caret Tutorial- 
the Basics.” On page 6 of the manual, it says “Navigate to the  
tutorial data set’s HUMAN_DATA/RIGHT_HEM directory.” But, there is  
no such directory in the extracted file. Did I download a wrong set  
of data?




Your help is greatly appreciated.



Ben

-

Benjamin Xu, Ph.D.

Human Cortical Physiology Section

National Institute of Neurological Disorders and Stroke

National Institutes of Health

5N234 Bldg 10 Center Dr.

Bethesda, MD 20892-1428

Phone: 301-402-7968



___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users

Re: [caret-users] help needed

[Donna Dierker]

Hi Shantanu,

There are a couple of ways to do this.  If you're lucky enough to have 
access to either a ROI or functional volume (e.g., AFNI +tlrc or FSL/SPM 
avg152 space group statistical output maps), then you can map them onto 
the PALS atlas using the procedure outlined in the PALS_B12 tutorial


http://sumsdb.wustl.edu:8081/sums/directory.do?dir_id=6332260

If you just have a stereotaxic coordinate, then you can use the Layers: 
Foci: Map Stereotaxic Focus feature.  See page 43 of this tutorial:


Caret 5.2 Tutorial - Introduction, Installation, Visualization, and 
Registration

http://brainmap.wustl.edu/caret/pdf/Caret_5_12_Tutorial_Intro.pdf

When doing metanalyses, one thing to keep in mind is that people use the 
term Talairach loosely.  They may call coordinates talairach, when 
they're really in another stereotaxic space (e.g., icbm 152 or Wash U's 
711-2B).  The PALS atlas contains several different average fiducial 
surfaces (in the Caret data_files/fmri_mapping_fils directory) to 
support various grids.  See this link for more details:


http://brainvis.wustl.edu/help/pals_volume_normalization/

When mapping foci or functional data, make sure you use the average 
fiducial surface that most closely resembles the space of your 
coordinates/volume.  If they're different, then your results are garbage.


On 04/26/2006 04:35 AM, shantanu ghosh wrote:


Dear Caret support
How can I paint  Talairach coordinates for different tasks with 
different colors onto a single cortical surface for illustration in 
metaanalysis?

thanks in advance,
shantanu


Shantanu Ghosh, PhD
Department of Humanities and Social Sciences
Indian Institute of Technology, Delhi
Hauz Khas
New Delhi 110016
INDIA
Tel.: +91-11-2659 6589
Fax: +91-11-2659 6509


Jiyo cricket on Yahoo! India cricket 

Yahoo! Messenger Mobile 
 
Stay in touch with your buddies all the time.




___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
 




--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)

Re: [caret-users] help needed

[shantanu ghosh]

Dear Caret support
  How can I paint  Talairach coordinates for different tasks with different 
colors onto a single cortical surface for illustration in metaanalysis?
  thanks in advance,
  shantanu


  Shantanu Ghosh, PhD
  Department of Humanities and Social Sciences
  Indian Institute of Technology, Delhi
  Hauz Khas
  New Delhi 110016
  INDIA
  Tel.: +91-11-2659 6589
  Fax: +91-11-2659 6509





-
 Jiyo cricket on Yahoo! India cricket
Yahoo! Messenger Mobile Stay in touch with your buddies all the time.

Re: [caret-users] help needed

[Donna Dierker]

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):


FAGPrecentral_L2001
FADPrecentral_R2002
F1GFrontal_Sup_L2101
...
VER8Vermis_89150
VER9Vermis_99160
VER10Vermis_109170

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 fo

RE: [caret-users] help needed

[Binyam Nardos]

Hi Donna,
I've managed to solve the second problem i.e.:

> 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.?
What I did to was load my regions of interest as a volume paint file instead of 
a functional volume file like I had initially done. I can now define different 
colors for each individual region.

Binyam

-Original Message-
From: [EMAIL PROTECTED] on behalf of Binyam Nardos
Sent: Wed 4/19/2006 10:16 AM
To: Caret, SureFit, and SuMS software users
Subject: RE: [caret-users] help needed
 

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):

FAGPrecentral_L2001
FADPrecentral_R2002
F1GFrontal_Sup_L2101
...
VER8Vermis_89150
VER9Vermis_99160
VER10Vermis_109170

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
>
>
>
>___
>caret-users mailing list
>caret-users@brainvis.wustl.edu
>http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>  
>

RE: [caret-users] help needed

[Binyam Nardos]

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):

FAGPrecentral_L2001
FADPrecentral_R2002
F1GFrontal_Sup_L2101
...
VER8Vermis_89150
VER9Vermis_99160
VER10Vermis_109170

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
>
>
>
>___
>caret-users mailing list
>caret-users@brainvis.wustl.edu
>http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>  
>


-- 
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)

___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users

<>

Re: [caret-users] help needed

[Donna Dierker]

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.




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):


FAGPrecentral_L2001
FADPrecentral_R2002
F1GFrontal_Sup_L2101
...
VER8Vermis_89150
VER9Vermis_99160
VER10Vermis_109170

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



___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
 




--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)

Re: [caret-users] help needed

[shantanu ghosh]

thanks, donna. I'll give it a try. 
  shantanu

Donna Dierker <[EMAIL PROTECTED]> wrote:
  Hi Shantanu,

>From your registration, I see you are using Windows XP. You will need 
Winzip or some other software that can extract zip archives. We 
typically extract the file "caret_distribution.v5.33.windows.zip" to the 
C: drive. When it extracts, it will create a caret folder under your C: 
drive. Then, you can create a shortcut to C:\caret\bin\caret5.exe on 
your desktop, or associate the extension ".spec" with the 
C:\caret\bin\caret5.exe executable, so that when you double-click on a 
spec file, Caret is launched.

After you get Caret installed, a good place to start is by taking the 
PALS tutorial:

http://sumsdb.wustl.edu/sums/directory.do?id=6332260

Click on the diskette-shaped icon to the left of these names:

PALS_ATLAS_CARET_5.3_TUTORIAL_June_05.pdf
PALS_TUTORIAL_DATA_JUNE_05.zip

Use Adobe Acrobat to view the PDF document, and use Winzip or other zip 
file extractor to unpack the .zip file dataset. The PDF document will 
walk you through the tutorial dataset.

On 04/10/2006 11:19 PM, shantanu ghosh wrote:

> i have downloaded the caret software from the site but i cannot 
> install it. how can i start?
> Shantanu
>
>
> Shantanu Ghosh, PhD
> Department of Humanities and Social Sciences
> Indian Institute of Technology, Delhi
> Hauz Khas
> New Delhi 110016
> INDIA
> Tel.: +91-11-2659 6589
> Fax: +91-11-2659 6509
>
> 
> Jiyo cricket on Yahoo! India cricket 
> 
> Yahoo! Messenger Mobile 
> 
> Stay in touch with your buddies all the time.
>
>
>
>___
>caret-users mailing list
>caret-users@brainvis.wustl.edu
>http://pulvinar.wustl.edu/mailman/listinfo/caret-users
> 
>
-- 

Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)

___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users



  Shantanu Ghosh, PhD
  Department of Humanities and Social Sciences
  Indian Institute of Technology, Delhi
  Hauz Khas
  New Delhi 110016
  INDIA
  Tel.: +91-11-2659 6589
  Fax: +91-11-2659 6509





-
 Jiyo cricket on Yahoo! India cricket
Yahoo! Messenger Mobile Stay in touch with your buddies all the time.

Re: [caret-users] help needed

[Donna Dierker]

Hi Shantanu,

From your registration, I see you are using Windows XP.  You will need 
Winzip or some other software that can extract zip archives.  We 
typically extract the file "caret_distribution.v5.33.windows.zip" to the 
C: drive.  When it extracts, it will create a caret folder under your C: 
drive.  Then, you can create a shortcut to C:\caret\bin\caret5.exe on 
your desktop, or associate the extension ".spec" with the 
C:\caret\bin\caret5.exe executable, so that when you double-click on a 
spec file, Caret is launched.


After you get Caret installed, a good place to start is by taking the 
PALS tutorial:


http://sumsdb.wustl.edu/sums/directory.do?id=6332260

Click on the diskette-shaped icon to the left of these names:

PALS_ATLAS_CARET_5.3_TUTORIAL_June_05.pdf
PALS_TUTORIAL_DATA_JUNE_05.zip

Use Adobe Acrobat to view the PDF document, and use Winzip or other zip 
file extractor to unpack the .zip file dataset.  The PDF document will 
walk you through the tutorial dataset.


On 04/10/2006 11:19 PM, shantanu ghosh wrote:

i have downloaded the caret software from the site but i cannot 
install it. how can i start?

Shantanu


Shantanu Ghosh, PhD
Department of Humanities and Social Sciences
Indian Institute of Technology, Delhi
Hauz Khas
New Delhi 110016
INDIA
Tel.: +91-11-2659 6589
Fax: +91-11-2659 6509


Jiyo cricket on Yahoo! India cricket 

Yahoo! Messenger Mobile 
 
Stay in touch with your buddies all the time.




___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
 


--

Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)

Re: [caret-users] help with mapping stereotaxic coordinates from a prior study

[Donna Hanlon]

Hi Dr. Labus,

The section on Foci in this manual should apply to Caret 5.3, since I 
don't believe much changed on the Layers: Foci menu:


Caret 5.2 Tutorial - Introduction, Installation, Visualization, and 
Registration

http://brainmap.wustl.edu/caret/pdf/Caret_5_12_Tutorial_Intro.pdf

Donna

On 08/23/2005 02:51 PM, J Labus wrote:

I would like to map new foci from research in my lab.  However I am 
having difficulty accomplishing this.  In the version 4 tutorial, 
there was a section entitled mapping new stereotaxic foci.  Is there 
similar documentation somewhere for version 5.3?



--
J Labus, PhD
Neuroimaging Core
UCLA Center for Neurovisceral Sciences and Women's Health
11301 Wilshire Blvd
Los Angeles, CA 90073
Office: (310) 478-3711 Ext. 41864
  Fax: (310) 794-2864 
--


___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users

Re: [caret-users] help finding handles

[Donna Hanlon]

Hi Marc,

Still, for the segmentation you sent me, caret is the better tool for 
finding and fixing the handles, which tough to see on the inflated surface.


cd SURFACES
caret5
File: Import VTK file:
   select left hem
   select topo and coords, deselect RGB colors
   
feb01_2003.L.full.segment_vent_corr.patch4_corr.patch3_corr.inflated-50.61838.vtk
Surface: Measurements: Crossover check, other type surface -- no 
crossovers, so re-running automatic error correction in SureFit probably 
would have been a waste of time.

File: Import Minc file:
   type anatomy
   ../feb01_2003.L.full.sMRI.mnc
File: Import Minc file:
   type segmentation
   
../SEGMENTATION/feb01_2003.L.full.segment_vent_corr.patch4_corr.patch3_corr.mnc

In the main window, switch to volume view.
If desired, Window: viewing Window 2 and switch window 2 to inflated 
surface view
In the main window, shift-left to pan the volume to the center of the 
window.
D/C : Overlay/Underlay Volume and select segmentation as the primary 
overlay,
Volume: Segmentation: Find handles: and select X, Y, and Z and Search 
for Handles; this will report the same handle in different slice views.

Click on the found handles, and the cursor will jump to that location.
Most of these handles shouldn't be filled; rather, they show where the 
calcarine sulcus has fused.  You need to zap voxles in those areas.  You 
can do this in caret or in SureFit, but if you do it in Caret, save your 
changes as an Analyze file, and do Analyze2Minc to convert it to minc. 
Then run Prepare for flattening in SureFit.


I don't pretend that this will be easy -- again, because the quality of 
the segmentation back there isn't great.


You might try adjusting your peaks a bit upward -- 92 and 71 rather than 
90 and 68.  You may have to repatch some of the same handles, but that 
calcarine handle does end up being smaller (and probably easier to 
patch) at the higher peaks.


Donna

On 09/08/2004 03:09 PM, Marc Malloy wrote:


Hi Donna
 
I'm having difficulties finding the reaming 4 handles with this data.  
I was wondering if you might take a look and point me in the right 
direction (I've messed with this for days with no luck).  I've 
uploaded the data in a zip file called marc.zip.  Thanks!
 
marc




___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users