Re: [caret-users] Caret Tutorial

[Donna Dierker]

On 11/28/2006 02:02 PM, Veronica S Smith wrote:

Hi,

I was just checking out the latest Caret Tutorial and wanted to 
clarify that the PDF file, "Caret_Tutorial_Oct6," is a companion to 
the archive, "CARET_TUTORIAL_SEPT06." It appears that the latter 
consists of data files only. Is that correct?

Yes -- correct.


Also, these two files are the most recent tutorials, yes?
Yes -- correct also.  The Oct 6 PDF reflects some typo and other minor 
document corrections noted at the MCW course in early October.


This is the latest and greatest dataset (same as in the 
CARET_TUTORIAL_SEPT-06 directory 
(http://sumsdb.wustl.edu/sums/directory.do?id=6585200 ):


CARET_TUTORIAL_SEPT06.zip
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595030


Thanks,
Veronica

[caret-users] Caret Tutorial

[Veronica S Smith]

Hi,

I was just checking out the latest Caret Tutorial and wanted to clarify that the PDF file, 
"Caret_Tutorial_Oct6," is a companion to the archive, "CARET_TUTORIAL_SEPT06." 
It appears that the latter consists of data files only. Is that correct?

Also, these two files are the most recent tutorials, yes?

Thanks,
Veronica

Re: [caret-users] Spherical registration

[Donna Dierker]

Mateus,

Yes -- that's the right archive.

I don't understand why you're getting the time out errors; I can't 
replicate the problem on my end.


What happens when you try this link (i.e., same, except port number 
omitted):


http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6057499

On 11/28/2006 01:03 PM, Mateus Joffily wrote:

Hi Donna,

I don't know if I am the only one experiencing this problem, but I am 
also unable to access the location: 
http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499. I 
still get a 'time out error'.


However, I can access the SuMS database from http://sumsdb.wustl.edu/. 
Could you, please, confirm me if this is the atlas that I need to 
download: 'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730'?


Thanks,
Mateus


Donna Dierker wrote:


On 11/28/2006 11:48 AM, Mateus Joffily wrote:


Hi,

I am a little bit confused on how to proceed to register an 
individual surface into an Atlas.
The 'Caret5 Tutorial: Segmentation, Flattening, and Registration' 
explains how to perform a spherical registration using the 
'Human.colin.L.REGISTER-to-INDIVIDUAL.03-05.71785.spec' file. My 
questions are:


1) What spec file should I use to register into the right hemisphere?
2) If I choose to register into PALS-B12 atlas, what files should I 
use?


The answer to both 1) and 2) is use the PALS_B12 LR combo 
registration target dataset:


http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499

And use the template deform_map included in that dataset to preset 
your registration parameters.  See this page and "Erin's cheat sheet" 
(linked from the page below) for more details:


http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html

This is what we do.  There are separate landmark datasets for the 
left and right, but they differ very little, and using the LR combo 
enables you to do cross-hem or inter-hem analyses.  The way we look 
at it, there's very little down side to using the combo dataset, but 
a lot of up side to doing so.  So we routinely use the LR combo now.


We stopped using colin as a registration target a couple of years 
ago, but some documentation may still refer to it.




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

Re: [caret-users] Spherical registration

[Mateus Joffily]

Hi Donna,

I don't know if I am the only one experiencing this problem, but I am 
also unable to access the location: 
http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499. I 
still get a 'time out error'.


However, I can access the SuMS database from http://sumsdb.wustl.edu/. 
Could you, please, confirm me if this is the atlas that I need to 
download: 'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730'?


Thanks,
Mateus


Donna Dierker wrote:


On 11/28/2006 11:48 AM, Mateus Joffily wrote:


Hi,

I am a little bit confused on how to proceed to register an 
individual surface into an Atlas.
The 'Caret5 Tutorial: Segmentation, Flattening, and Registration' 
explains how to perform a spherical registration using the 
'Human.colin.L.REGISTER-to-INDIVIDUAL.03-05.71785.spec' file. My 
questions are:


1) What spec file should I use to register into the right hemisphere?
2) If I choose to register into PALS-B12 atlas, what files should I use?


The answer to both 1) and 2) is use the PALS_B12 LR combo registration 
target dataset:


http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499

And use the template deform_map included in that dataset to preset 
your registration parameters.  See this page and "Erin's cheat sheet" 
(linked from the page below) for more details:


http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html

This is what we do.  There are separate landmark datasets for the left 
and right, but they differ very little, and using the LR combo enables 
you to do cross-hem or inter-hem analyses.  The way we look at it, 
there's very little down side to using the combo dataset, but a lot of 
up side to doing so.  So we routinely use the LR combo now.


We stopped using colin as a registration target a couple of years ago, 
but some documentation may still refer to it.




Thanks,
Mateus
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Re: [caret-users] Spherical registration

[Donna Dierker]

On 11/28/2006 11:48 AM, Mateus Joffily wrote:

Hi,

I am a little bit confused on how to proceed to register an individual 
surface into an Atlas.
The 'Caret5 Tutorial: Segmentation, Flattening, and Registration' 
explains how to perform a spherical registration using the 
'Human.colin.L.REGISTER-to-INDIVIDUAL.03-05.71785.spec' file. My 
questions are:


1) What spec file should I use to register into the right hemisphere?
2) If I choose to register into PALS-B12 atlas, what files should I use?
The answer to both 1) and 2) is use the PALS_B12 LR combo registration 
target dataset:


http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499

And use the template deform_map included in that dataset to preset your 
registration parameters.  See this page and "Erin's cheat sheet" (linked 
from the page below) for more details:


http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html

This is what we do.  There are separate landmark datasets for the left 
and right, but they differ very little, and using the LR combo enables 
you to do cross-hem or inter-hem analyses.  The way we look at it, 
there's very little down side to using the combo dataset, but a lot of 
up side to doing so.  So we routinely use the LR combo now.


We stopped using colin as a registration target a couple of years ago, 
but some documentation may still refer to it.


Thanks,
Mateus
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caret-users@brainvis.wustl.edu
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[caret-users] Spherical registration

[Mateus Joffily]

Hi,

I am a little bit confused on how to proceed to register an individual 
surface into an Atlas.
The 'Caret5 Tutorial: Segmentation, Flattening, and Registration' 
explains how to perform a spherical registration using the 
'Human.colin.L.REGISTER-to-INDIVIDUAL.03-05.71785.spec' file. My 
questions are:


1) What spec file should I use to register into the right hemisphere?
2) If I choose to register into PALS-B12 atlas, what files should I use?

Thanks,
Mateus

Re: [caret-users] caret on AMD64

[marco tettamanti]

Dear Volkmar, John and Donna,
this is an old thread, but I just wanted to say that I eventually found 
some time to get back to my problem of running caret on an AMD64 
architecture and solved it: the solution proposed by Volkmar did the 
trick! This basically amounted to run ldd caret5 and install the missing 
32-bit libraries with the following commands:


yum install libpng.i386
yum install xorg-x11-libs.i386
yum install xorg-x11-Mesa-libGLU.i386

Now everything's running properly. All the best!
Marco


Marco Tettamanti wrote:



*/Volkmar Glauche <[EMAIL PROTECTED]>/* wrote:

Dear Marco & others,

it appears that your caret5 is a 32-bit executable. At least it is
for my
binary 5.3 distribution.

file caret5

should tell you what your system thinks of the binary format, and
the ldd
output suggests that only 32-bit libraries are used. To use this binary
as it is, you will have to install the whole bunch of 32-bit shared
libraries it needs. Or go and recompile, but then you will need to
install
the development files for these libraries.

Volkmar

On Wed, 30 Aug 2006, Marco Tettamanti wrote:

 > Hi Donna and John,
 > thank you for your answers! Unfortunately I couldn't solve the
problem.
 >
 > I have tried exporting /usr/lib64 to LD_LIBRARY_PATH, but I still
get the same error message:
 > "error while loading shared libraries: libpng12.so.0: cannot open
shared object file: No such file or directory"
 >
 > The output of ldd caret5 is:
 >
 > [EMAIL PROTECTED] bin]# ldd caret5
 > linux-gate.so.1 => (0xe000)
 > libpng12.so.0 => not found
 > libSM.so.6 => not found
 > libICE.so.6 => not found
 > libXi.so.6 => not found
 > libXrender.so.1 => not found
 > libXrandr.so.2 => not found
 > libXcursor.so.1 => not found
 > libfreetype.so.6 => not found
 > libfontconfig.so.1 => not found
 > libXext.so.6 => not found
 > libX11.so.6 => not found
 > libz.so.1 => not found
 > libpthread.so.0 => /lib/tls/libpthread.so.0 (0xf7fdb000)
 > libdl.so.2 => /lib/libdl.so.2 (0xf7fd7000)
 > libGLU.so.1 => not found
 > libGL.so.1 => /usr/lib/libGL.so.1 (0xf7f51000)
 > libm.so.6 => /lib/tls/libm.so.6 (0xf7f2e000)
 > libc.so.6 => /lib/tls/libc.so.6 (0x00669000)
 > /lib/ld-linux.so.2 (0x0065)
 > libGLcore.so.1 => /usr/lib/libGLcore.so.1 (0xf776c000)
 > libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0xf776a000)
 > libXext.so.6 => not found
 > libX11.so.6 => not found
 >
 > I have tried creating a symolic link to the existing
/usr/lib64/libpng12.so.0 both in the /lib and /usr/lib directories,
but I still get the same error message.
 > Permissions and file integrity should all be ok.
 >
 > Do you have any other suggestions?
 > Thank you a lot!
 > Marco
 >
 >
 >
 > Marco Tettamanti wrote:
 >
 >
 > */Donna Dierker /* wrote:
 >
 > Date: Tue, 29 Aug 2006 08:47:13 -0500
 > From: Donna Dierker
 > To: "Caret, SureFit, and SuMS software users"
 >
 > Subject: Re: [caret-users] [SPAM] caret on AMD64
 >
 > Try making sure /usr/lib64 is in your LD_LIBRARY_PATH variable,
e.g.:
 >
 > setenv LD_LIBRARY_PATH /usr/lib64:$LD_LIBRARY_PATH
 >
 > ... or if your shell is bash:
 >
 > export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH
 >
 > Thanks for reporting the issue with the mailing list. It sounds
like I
 > need to check the spam settings for [EMAIL PROTECTED]
 >
 > On 08/29/2006 03:01 AM, Marco Tettamanti wrote:
 > > Dear Donna and John,
 > > first of all I would like to express my congratulations for the
 > > improvements you made in Caret! I haven't been using the
software for
 > > some times, but now that I have some new data to work on and I
have
 > > started to use the latest release (5.4), I find that many options
 > have
 > > been made more intuitive and easy to use, especially for the
manual
 > > correction of segmentation errors.
 > >
 > > I am trying to install caret on an an AMD64 linux architecture
 > (CentOS
 > > 4.3, kernel 2.6.9, 2 x AMD Opteron dual-core).
 > > I have tried installing from the linux binaries, but I receive an
 > error
 > > message that some libraries cannot be opened ("error while loading
 > > shared libraries: libpng12.so.0: cannot open shared object file:
 > No such
 > > file or directory"), even if I create symbolic links to e.g.
 > > /usr/lib64/libpng12.so.0.
 > > Is there any way I can get the caret binaries to work on AMD64,
 > without
 > > having to build from the source files?
 > >
 > > Thank you a lot for your help,
 > > Marco
 > >
 > > P.S.: I am using this alternative email address because but I have
 > > tried several times to send an

Re: [caret-users] SuMS

[Mateus Joffily]

Hi Donna,

http://sumsdb.wustl.edu is working.
The links from 
http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html are 
not working for me. I always get the same error:

"The connection has timed out
The server at sumsdb.wustl.edu is taking too long to respond."

I have already got to download the specs that I need. Thanks.

Mateus

Donna Dierker wrote:


Hi Mateus,

Try http://sumsdb.wustl.edu instead of 
http://brainmap.wustl.edu/sums.  The latter should redirect to the 
former, but evidently that isn't happening in your case.  I'm copying 
Ping Gu, our sumsdb developer, so she can track down the trouble.


I think those links (with the sumsdb hostname) are available here:

http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html

On 11/27/2006 11:13 AM, Mateus Joffily wrote:


Hi,

Since last week, I am trying to connect to SumsDB homepage 
(http://brainmap.wustl.edu/sums), but I always get a time out 
connection. Could you, please, confirm me if it is online? I need to 
download:


* Colin ref-for-landmarks left:
  Human.colin.LEFT.REG-with-PALS-B12.71785.spec
  



* Colin ref-for-landmarks right:
  Human.colin.RIGHT.REG-with-PALS-B12.71723.spec
  



to help me drawing the registration borders.

Thanks,
Mateus


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Re: [caret-users] question about documentation

[Donna Dierker]

On 11/28/2006 03:32 AM, Andrew Reid wrote:

Question about documentation:

Does a documentation file exist that outlines each of the various file 
types used in Caret, including:


What sort of information is being represented by the data
How this data is used by Caret
How the file types interact (e.g., how area colour files are used by 
probabilistic atlas files, etc.)
File formats: 
http://brainmap.wustl.edu/caret/caret5.5_help/file_formats/file_formats.html
File types: 
http://brainmap.wustl.edu/caret/caret5.5_help/file_formats/files.html
What sort of info is represented by the data:  Probably the best doc for 
this is the 9/2006 tutorial:


CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu/sums/directory.do?id=6585200

A quick summary:

paint = discrete/categorical/ROI attributes by node
metric = scalar for each node, typically functional -- used often as 
"overlay"
surface_shape = scalar for each node, typically anatomical -- used often 
as "underlay"


Note: metric and surface_shape formats are identical, so you can open 
one file as the other type.


Areacolor maps paint names to colors; palette defines same for metric/shape.


?

Basically, I'm looking for a straightforward description of the 
application in terms of its data model, its I/O model, and how it is 
organized. The tutorials are great for specific purposes, but in my 
case I'd much rather have an understanding of the application and 
figure out the tools based upon this.
Sorry, nothing like the ITK software developer's guide, if that's what 
you're looking for.


Specifically, I would like to be able to compare a delineated lesion - 
registered to a template - to a probabilistic atlas, in order to get a 
set of nodes in the PALS surface representing the lesion extents 
within the cortical sheet, with each node pointing to a probability 
value of being situated in a specific anatomical structure. This way I 
can get an idea of which structures are being disrupted by the lesion, 
and with what probability.
This seems doable, provided you segment your lesioned brain and register 
it to PALS_B12, which may prove challenging.  We're grappling with 
similar applications on our end.  I'm not sure how far anyone has gotten 
with this on sizable lesions.  Anyone who has done this is encouraged to 
share your experience.


I've been playing with the tutorials and various datasets, but can't 
seem to get an understanding of how these probabilistic atlas files 
work, and how to go from my delineated lesion to a probabilistic 
mapping of this lesion.
So you could, in theory, map a ROI paint volume of your lesion onto the 
PALS_B12 average fiducial surface in the same space as your ROI. Or map 
it as a functional volume, if that proves problematic.  Then use 
Surface: ROI to threshold the resulting metric (or just select the 
paint, if mapped as ROI paint) and do generate report on selected nodes, 
with the probabilistic atlas surface loaded.  I'm not sure exactly how 
this would work, or if the result would be sensible, but have you tried 
something like this?


Thanks in advance!
Andrew


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

Re: [caret-users] SuMS

[Donna Dierker]

Hi Mateus,

Try http://sumsdb.wustl.edu instead of http://brainmap.wustl.edu/sums.  
The latter should redirect to the former, but evidently that isn't 
happening in your case.  I'm copying Ping Gu, our sumsdb developer, so 
she can track down the trouble.


I think those links (with the sumsdb hostname) are available here:

http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html

On 11/27/2006 11:13 AM, Mateus Joffily wrote:

Hi,

Since last week, I am trying to connect to SumsDB homepage 
(http://brainmap.wustl.edu/sums), but I always get a time out 
connection. Could you, please, confirm me if it is online? I need to 
download:


* Colin ref-for-landmarks left:
  Human.colin.LEFT.REG-with-PALS-B12.71785.spec
  

* Colin ref-for-landmarks right:
  Human.colin.RIGHT.REG-with-PALS-B12.71723.spec
  

to help me drawing the registration borders.

Thanks,
Mateus


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

[caret-users] question about documentation

[Andrew Reid]

Question about documentation:

Does a documentation file exist that outlines each of the various file 
types used in Caret, including:


What sort of information is being represented by the data
How this data is used by Caret
How the file types interact (e.g., how area colour files are used by 
probabilistic atlas files, etc.)


?

Basically, I'm looking for a straightforward description of the 
application in terms of its data model, its I/O model, and how it is 
organized. The tutorials are great for specific purposes, but in my case 
I'd much rather have an understanding of the application and figure out 
the tools based upon this.


Specifically, I would like to be able to compare a delineated lesion - 
registered to a template - to a probabilistic atlas, in order to get a 
set of nodes in the PALS surface representing the lesion extents within 
the cortical sheet, with each node pointing to a probability value of 
being situated in a specific anatomical structure. This way I can get an 
idea of which structures are being disrupted by the lesion, and with 
what probability.


I've been playing with the tutorials and various datasets, but can't 
seem to get an understanding of how these probabilistic atlas files 
work, and how to go from my delineated lesion to a probabilistic mapping 
of this lesion.


Thanks in advance!
Andrew

--
Andrew Reid
Department of Cognitive Neuroscience
Radboud University Nijmegen Medical Centre
Postbus 9101, 6500 HB Nijmegen
The Netherlands

phone +31 24 3666171