Re: [caret-users] About Monkey to Human Deformation

[Donna Dierker]

Hi Reza,

See inline reply below.

Donna

On 03/14/2007 03:40 PM, Reza Rajimehr wrote:

Hi Donna,

The Data File button is disabled in my Caret, so I think I have to use the
caret commands. Just a question: what are "source" and "target" paths in
the first caret command. I assume that the source path is a monkey
(macaque F99) directory, which has the input metric file, and the target
path is a human PALS directory. Is this correct?
  
Correct, but in this case, I'm wondering whether you can set both source 
and target directories to CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN 
and simply use the deform_map in that directory.


This directory contains some, but not all of the source and target files 
cited in the deform_map file.

I have already added the .deform_map file to the directory, which has the
input metric file.
  
This is not normally necessary.  Typically, the file you want to deform 
is in the source directory, while the deform_map you use is in the 
target (atlas) directory.  The output file (usually the same as the 
input file with "deformed_" prepended) usually is written to the atlas 
target directory.


But in your case, setting both source and target directories to the 
absolute path of your CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN 
directory may work.  Then you could navigate to your data file as 
needed, and let Caret write your deformed data file to your 
CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN directory.

Thanks for your help,
Reza


  

Hi Reza,

Hmmm.  I can almost replicate this behavior.  When I load
CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN/RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-LDMK-VE.73730.spec.deform_map,
both the individual and atlas directory buttons are disabled, but Data
File and Deformed File... are both enabled (see attached capture).  I
thought perhaps this might be because the deform_map was read-only, but
I get the same behavior with a copy that is writeable.  Normally, one
can change the individual and atlas directories, as one must do when
using a deform_map from one of our datasets (unless you're David Van
Essen, in which case the paths work fine).

Using the Data File button, I could navigate to an input metric and
successfully deform the data file.  But if your buttons are disabled,
then you might try using the following two caret commands to get the job
done:

   DEFORMATION MAP FILE SOURCE/TARGET PATH UPDATE
  caret_command -def-map-path \
   

   SURFACE APPLY DEFORMATION MAP
  caret_command -surface-deformation-apply \
   \
\
 [source-topo-file]  [source-deformed-topo-file] \
 [atlas-topo-file]

  Deform a data file.

  Note: "source-topo-file", "source-deformed-topo-file" and
  "atlas-topo-file" are only required when deforming
  coordinate files.

  "file-type" is one of:
 AREAL_ESTIMATION
 BORDER_FLAT
 BORDER_PROJECTION
 BORDER_SPHERICAL
 CELL
 CELL_PROJECTION
 COORDINATE
 COORDINATE_FLAT
 FOCI
 FOCI_PROJECTION
 LAT_LON
 METRIC
 PAINT
 PROB_ATLAS
 RGB_PAINT
 SURFACE_SHAPE
 TOPOGRAPHY

Donna

On 03/14/2007 03:11 AM, Reza Rajimehr wrote:


Dear David,

In the "Apply Deformation Map" dialog box, I specified the following
items:

1) Deformation Map File: the 23-LDMK deform_map file
2) File Type: Metric
3) Flat Max Edge Length: 10.00
4) Metric Deformation: Nearest Node (not sure which one is better?)
5) Smooth One Iteration (Except Flat)

The other buttons were not clickable (the dialog box does not allow me
to
use them).

When I click the "Apply" button, I immediately receive the following
error
message:

Deform Error
Is deformation map file valid? You must select a data file for
deformation. You must select the output name for the deformed file.

I tried to apply deformation map from two different .spec files:

1) Macaque F99 atlas directory, which has deformed metric files (from
individual macaque to F99). I added/appended the .deform_map file to
this
.spec file before applying deformation.

2) COMPARE_MACAQUE_HUMAN directory (as a part of CARET_TUTORIAL_SEPT06
directory). I added/appended my metric files to this .spec file before
applying deformation.

In both cases, I got the same error.


Thanks for your helpful comments/suggestions,

Reza



  

Reza,

On Mar 10, 2007, at 9:31 PM, Reza Rajimehr wrote:




Dear caret-users,

David Van Essen suggested me to use the following .deform_map file for
deformation of macaque F99 to Human PALS:

RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-
LDMK-VE.73730.spec.deform_map

  

Once you have a deform_map file, you can use it to register data
sets  from monkey to human WITHOUT re-running a registration.  This
is done using the Surface: Deformation: Apply Deformation Map
option.  If you want to register paint files, metric files, a

Re: [caret-users] About Monkey to Human Deformation

[John Harwell]

On Mar 14, 2007, at 3:40 PM, Reza Rajimehr wrote:



The Data File button is disabled in my Caret, so I think I have to  
use the

caret commands.


Reza,

The Data File button will be enabled once a deformation map file has  
been loaded.  To load a deformation map file, press the "Deformation  
Map File" button and select the deformation map file that was  
produced by the deformation process.


John

Re: [caret-users] About Monkey to Human Deformation

[Reza Rajimehr]

Hi Donna,

The Data File button is disabled in my Caret, so I think I have to use the
caret commands. Just a question: what are "source" and "target" paths in
the first caret command. I assume that the source path is a monkey
(macaque F99) directory, which has the input metric file, and the target
path is a human PALS directory. Is this correct?

I have already added the .deform_map file to the directory, which has the
input metric file.

Thanks for your help,
Reza


> Hi Reza,
>
> Hmmm.  I can almost replicate this behavior.  When I load
> CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN/RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-LDMK-VE.73730.spec.deform_map,
> both the individual and atlas directory buttons are disabled, but Data
> File and Deformed File... are both enabled (see attached capture).  I
> thought perhaps this might be because the deform_map was read-only, but
> I get the same behavior with a copy that is writeable.  Normally, one
> can change the individual and atlas directories, as one must do when
> using a deform_map from one of our datasets (unless you're David Van
> Essen, in which case the paths work fine).
>
> Using the Data File button, I could navigate to an input metric and
> successfully deform the data file.  But if your buttons are disabled,
> then you might try using the following two caret commands to get the job
> done:
>
>DEFORMATION MAP FILE SOURCE/TARGET PATH UPDATE
>   caret_command -def-map-path \
>
>
>SURFACE APPLY DEFORMATION MAP
>   caret_command -surface-deformation-apply \
>\
> \
>  [source-topo-file]  [source-deformed-topo-file] \
>  [atlas-topo-file]
>
>   Deform a data file.
>
>   Note: "source-topo-file", "source-deformed-topo-file" and
>   "atlas-topo-file" are only required when deforming
>   coordinate files.
>
>   "file-type" is one of:
>  AREAL_ESTIMATION
>  BORDER_FLAT
>  BORDER_PROJECTION
>  BORDER_SPHERICAL
>  CELL
>  CELL_PROJECTION
>  COORDINATE
>  COORDINATE_FLAT
>  FOCI
>  FOCI_PROJECTION
>  LAT_LON
>  METRIC
>  PAINT
>  PROB_ATLAS
>  RGB_PAINT
>  SURFACE_SHAPE
>  TOPOGRAPHY
>
> Donna
>
> On 03/14/2007 03:11 AM, Reza Rajimehr wrote:
>> Dear David,
>>
>> In the "Apply Deformation Map" dialog box, I specified the following
>> items:
>>
>> 1) Deformation Map File: the 23-LDMK deform_map file
>> 2) File Type: Metric
>> 3) Flat Max Edge Length: 10.00
>> 4) Metric Deformation: Nearest Node (not sure which one is better?)
>> 5) Smooth One Iteration (Except Flat)
>>
>> The other buttons were not clickable (the dialog box does not allow me
>> to
>> use them).
>>
>> When I click the "Apply" button, I immediately receive the following
>> error
>> message:
>>
>> Deform Error
>> Is deformation map file valid? You must select a data file for
>> deformation. You must select the output name for the deformed file.
>>
>> I tried to apply deformation map from two different .spec files:
>>
>> 1) Macaque F99 atlas directory, which has deformed metric files (from
>> individual macaque to F99). I added/appended the .deform_map file to
>> this
>> .spec file before applying deformation.
>>
>> 2) COMPARE_MACAQUE_HUMAN directory (as a part of CARET_TUTORIAL_SEPT06
>> directory). I added/appended my metric files to this .spec file before
>> applying deformation.
>>
>> In both cases, I got the same error.
>>
>>
>> Thanks for your helpful comments/suggestions,
>>
>> Reza
>>
>>
>>
>>> Reza,
>>>
>>> On Mar 10, 2007, at 9:31 PM, Reza Rajimehr wrote:
>>>
>>>
 Dear caret-users,

 David Van Essen suggested me to use the following .deform_map file for
 deformation of macaque F99 to Human PALS:

 RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-
 LDMK-VE.73730.spec.deform_map

>>> Once you have a deform_map file, you can use it to register data
>>> sets  from monkey to human WITHOUT re-running a registration.  This
>>> is done using the Surface: Deformation: Apply Deformation Map
>>> option.  If you want to register paint files, metric files, and most
>>> other files, you don't need anything other than the deform_map file
>>> to get the job done, and the dialog window is fairly self-
>>> explanatory.  If you want to register a border projection file or a
>>> coordinate file, then you need additional coordinate and topology
>>> files that are available as part of the Caret Sept_06 tutorial dataset:
>>> http://sumsdb.wustl.edu/sums/archivelist.do?
>>> archive_id=6595051&archive_name=COMPARE_PALS_MacaqueF99.73730.spec
>>>
>>> The only reason to actually re-run an interspecies registration is IF
>>> you don't like the particular set of landmarks used and you want to
>>> try your own.  If so, you should start with borderproj files also in:
>>> http://sumsdb.wustl.edu/sums/archivelist.do?
>>> archive_id=

Re: [caret-users] Monkey Atlas and stereotaxic

[Donna Dierker]

Hi Remya,

Glad to hear you got your hands on a T1 scan.

There's no documentation I know of that covers what you want to do, but 
it's not that hard (if I understand it correctly).


I think you'll just need two versions of your volumes (one AC-centered, 
one inter-aural) and two versions of your fiducial surface (ditto).  
You'll need the AC-centered volume to create your fiducial surface, 
which also will be AC-centered.  When you're happy with your AC-centered 
surface, then translate both volume and surface back to inter-aural.


The hard part is calculating the x,y,z translation offsets between the 
AC-centered origin and your inter-aural origin.  Sometimes it takes a 
sign flip or two to get it right, but only you can compute the magnitude 
of these shifts.  I'll call them shiftx, shifty, shiftz.


Change your volume back to inter-aural like so:

Volume: Edit volume attributes: coordinates: origin: Adjust x,y,z by 
shiftx,shifty,shiftz.  After applying change, hit toolbar: R (with 
volume view in main window) to reset the volume to the new origin, to 
make sure it's correct.  This may take trial and error to get the sign 
right.


Once the volume view accurately reflects the inter-aural origin, save 
the translated volume: File: Save Data File: volume files: NIFTI (or 
AFNI or SPM/MedX, which is basically Analyze): my_interaural.nii


Now, translate your surface:

* switch to fiducial view in main window
* Window: Transformation matrix editor
* Translate: enter shiftx, shifty, shiftz (again -- sign-flipping as needed)
* Apply matrix to main window

In this case, if you get it wrong, then you'll need to use Toolbar: spec 
to reload the fiducial after each trial, to get back to the original AC 
origin.


Once you get it right, use File: Save data file: coord file to save the 
translated coord file as a name like my.fiducial.inter-aural.coord.


Good luck.

Donna

On 03/14/2007 02:44 PM, Remya Nair wrote:

Hi Caret-Gods...!

I have a question regarding Caret and monkey atlas. I apologize for 
the basic nature of these questions, but I am a newbie to Caret and 
that is all i have to say in my defense!!!
We have T1 weighted 0.5 isotropic resolution anatomical images of 
monkey brain. The final aim is to be able to reconstruct surfaces as 
well as find the co-ordinates of points of interest w.r.t our 
stereotaxic coord system. We are working with the inter-aural 
stereotaxic system.
Ideally, apart from viewing the surface , we will need stereotaxic 
coordinates to know exactly where the AP0 is, mediolateral coordinates 
etc.
I have ,as per the Caret segmentation tutorial, segmented the volume 
and created the surfaces. But, the way i have done it, the volume has 
been centered at the AC (as per the tutorial instructions). What 
should I do to center it to the inter-aural origin? is there any caret 
documentation on this... if yes, could you please point me to them? 
Consequently what would be the next steps I should perform (perhaps 
registration?) to be able to read off the stereo-coords of interest as 
per my coordinate system? Please do point me to the appropriate 
tutorials/spec files that i may need.


Thanks in advance!!

RN

[caret-users] Monkey Atlas and stereotaxic

[Remya Nair]

Hi Caret-Gods...!

I have a question regarding Caret and monkey atlas. I apologize for  
the basic nature of these questions, but I am a newbie to Caret and  
that is all i have to say in my defense!!!
We have T1 weighted 0.5 isotropic resolution anatomical images of  
monkey brain. The final aim is to be able to reconstruct surfaces as  
well as find the co-ordinates of points of interest w.r.t our  
stereotaxic coord system. We are working with the inter-aural  
stereotaxic system.
Ideally, apart from viewing the surface , we will need stereotaxic  
coordinates to know exactly where the AP0 is, mediolateral  
coordinates etc.
I have ,as per the Caret segmentation tutorial, segmented the volume  
and created the surfaces. But, the way i have done it, the volume has  
been centered at the AC (as per the tutorial instructions). What  
should I do to center it to the inter-aural origin? is there any  
caret documentation on this... if yes, could you please point me to  
them? Consequently what would be the next steps I should perform  
(perhaps registration?) to be able to read off the stereo-coords of  
interest as per my coordinate system? Please do point me to the  
appropriate tutorials/spec files that i may need.


Thanks in advance!!

RN

Re: [caret-users] Announcement: open access MR data (OASIS)

[Donna Dierker]

In case it becomes useful to anyone, these 12 OASIS subjects comprise 
the PALS_B12:


OAS1_0006_MR1 Human_Buckner_Case06
OAS1_0009_MR1 Human_Buckner_Case04
OAS1_0054_MR1 Human_Buckner_Case01
OAS1_0061_MR1 Human_Buckner_Case11
OAS1_0111_MR1 Human_Buckner_Case07
OAS1_0152_MR1 Human_Buckner_Case05
OAS1_0163_MR1 Human_Buckner_Case03
OAS1_0350_MR1 Human_Buckner_Case08
OAS1_0361_MR1 Human_Buckner_Case10
OAS1_0368_MR2 Human_Buckner_Case12
OAS1_0448_MR1 Human_Buckner_Case02
OAS1_0450_MR1 Human_Buckner_Case09

Donna Dierker
http://brainmap.wustl.edu/

On 03/14/2007 12:37 PM, Daniel Marcus wrote:


Dear Colleagues,

The Open Access Series of Imaging Studies (OASIS) is now available at 
www.oasis-brains.org . The data are 
publicly available under to a liberal Data Use Agreement available 
here: http://www.oasis-brains.org/app/template/UsageAgreement.vm. The 
first data set includes structural MR obtained from 416 subjects aged 
18 to 96, including 100 subjects diagnosed with very mild to moderate 
Alzheimer’s Disease. A longitudinal data set will be released in the 
coming months. A manuscript describing the project is currently in 
press at Journal of Cognitive Neuroscience. For more information, 
please visit the website.


Regards,

Dan Marcus

[EMAIL PROTECTED]

Neuroinformatics Research Group

Washington University School of Medicine

http://nrg.wustl.edu 

[caret-users] Announcement: open access MR data (OASIS)

[Daniel Marcus]

Dear Colleagues,

 

The Open Access Series of Imaging Studies (OASIS) is now available at
www.oasis-brains.org  .  The data are
publicly available under to a liberal Data Use Agreement available here:
http://www.oasis-brains.org/app/template/UsageAgreement.vm.  The first
data set includes structural MR obtained from 416 subjects aged 18 to
96, including 100 subjects diagnosed with very mild to moderate
Alzheimer's Disease.  A longitudinal data set will be released in the
coming months.  A manuscript describing the project is currently in
press at Journal of Cognitive Neuroscience.  For more information,
please visit the website.

 

Regards,

Dan Marcus

[EMAIL PROTECTED]

Neuroinformatics Research Group

Washington University School of Medicine

http://nrg.wustl.edu  

 

 

Re: [caret-users] About Monkey to Human Deformation

[John Harwell]

Reza,

Did you press the "Data File..." button to choose an input metric  
file for deformation?  The Apply Deformation Map Dialog requires the  
user to select one specific data file for deformation, it does not  
deform all of the files automatically which is done as part of the  
spherical registration.


--
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 Mar 14, 2007, at 3:11 AM, Reza Rajimehr wrote:


Dear David,

In the "Apply Deformation Map" dialog box, I specified the  
following items:


1) Deformation Map File: the 23-LDMK deform_map file
2) File Type: Metric
3) Flat Max Edge Length: 10.00
4) Metric Deformation: Nearest Node (not sure which one is better?)
5) Smooth One Iteration (Except Flat)

The other buttons were not clickable (the dialog box does not allow  
me to

use them).

When I click the "Apply" button, I immediately receive the  
following error

message:

Deform Error
Is deformation map file valid? You must select a data file for
deformation. You must select the output name for the deformed file.

I tried to apply deformation map from two different .spec files:

1) Macaque F99 atlas directory, which has deformed metric files (from
individual macaque to F99). I added/appended the .deform_map file  
to this

.spec file before applying deformation.

2) COMPARE_MACAQUE_HUMAN directory (as a part of CARET_TUTORIAL_SEPT06
directory). I added/appended my metric files to this .spec file before
applying deformation.

In both cases, I got the same error.


Thanks for your helpful comments/suggestions,

Reza



Reza,

On Mar 10, 2007, at 9:31 PM, Reza Rajimehr wrote:


Dear caret-users,

David Van Essen suggested me to use the following .deform_map  
file for

deformation of macaque F99 to Human PALS:

RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-
LDMK-VE.73730.spec.deform_map


Once you have a deform_map file, you can use it to register data
sets  from monkey to human WITHOUT re-running a registration.  This
is done using the Surface: Deformation: Apply Deformation Map
option.  If you want to register paint files, metric files, and most
other files, you don't need anything other than the deform_map file
to get the job done, and the dialog window is fairly self-
explanatory.  If you want to register a border projection file or a
coordinate file, then you need additional coordinate and topology
files that are available as part of the Caret Sept_06 tutorial  
dataset:

http://sumsdb.wustl.edu/sums/archivelist.do?
archive_id=6595051&archive_name=COMPARE_PALS_MacaqueF99.73730.spec

The only reason to actually re-run an interspecies registration is IF
you don't like the particular set of landmarks used and you want to
try your own.  If so, you should start with borderproj files also in:
http://sumsdb.wustl.edu/sums/archivelist.do?
archive_id=6595051&archive_name=COMPARE_PALS_MacaqueF99.73730.spec
and make your additions and subtractions from there.

See Part 4 of the latest Caret tutorial for more details on monkey-
human comparisons.
http://sumsdb.wustl.edu/sums/directory.do?
id=6585200&dir_name=CARET_TUTORIAL_SEPT-06



I specified this as my .deform_map file in the Spherical Parameters
tab in
the Spherical Surface Deformation dialog box. My question is what I
should
specify as .borderproj file. I have a borderproj file in my F99
directory
(that I used for the registration of individual macaque to F99). I
also
have a borderproj file in my PALS directory (that I used for the
registration of individual human to PALS). Should I use these
borderproj
files in the Individual and Atlas tabs in the Spherical Surface
Deformation dialog box? Or there are other files that I should use?

I also assume that the macaque F99 .spec file should be used in the
Individual tab, and the human PALS .spec file should be used in the
Atlas
tab.


See above.  These steps should not be necessary for your purposes.

I hope this helps.

David



Thanks for your help,
Reza


Reza Rajimehr, MD

NMR Athinoula A. Martinos Center
Department of Radiology
Massachusetts General Hospital (MGH)
Building 149, 13th St.
Charlestown, MA 02129

Email: [EMAIL PROTECTED]

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


___
caret-users mailing list
caret-users@brainvis.wustl.edu
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Reza Rajimehr, MD

NMR Athinoula A. Martinos Center
Department of Radiology
Massachusetts General Hospital (MGH)
Building 149, 13th St.
Charlestown, MA 02129

Email: [EMAIL PROTECTED]

Re: [caret-users] About Monkey to Human Deformation

[Donna Dierker]

Hi Reza,

Hmmm.  I can almost replicate this behavior.  When I load 
CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN/RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-LDMK-VE.73730.spec.deform_map, 
both the individual and atlas directory buttons are disabled, but Data 
File and Deformed File... are both enabled (see attached capture).  I 
thought perhaps this might be because the deform_map was read-only, but 
I get the same behavior with a copy that is writeable.  Normally, one 
can change the individual and atlas directories, as one must do when 
using a deform_map from one of our datasets (unless you're David Van 
Essen, in which case the paths work fine).


Using the Data File button, I could navigate to an input metric and 
successfully deform the data file.  But if your buttons are disabled, 
then you might try using the following two caret commands to get the job 
done:


  DEFORMATION MAP FILE SOURCE/TARGET PATH UPDATE
 caret_command -def-map-path \
  

  SURFACE APPLY DEFORMATION MAP
 caret_command -surface-deformation-apply \
  \
   \
[source-topo-file]  [source-deformed-topo-file] \
[atlas-topo-file]
   
 Deform a data file.


 Note: "source-topo-file", "source-deformed-topo-file" and
 "atlas-topo-file" are only required when deforming
 coordinate files.

 "file-type" is one of:
AREAL_ESTIMATION
BORDER_FLAT
BORDER_PROJECTION
BORDER_SPHERICAL
CELL
CELL_PROJECTION
COORDINATE
COORDINATE_FLAT
FOCI
FOCI_PROJECTION
LAT_LON
METRIC
PAINT
PROB_ATLAS
RGB_PAINT
SURFACE_SHAPE
TOPOGRAPHY

Donna

On 03/14/2007 03:11 AM, Reza Rajimehr wrote:

Dear David,

In the "Apply Deformation Map" dialog box, I specified the following items:

1) Deformation Map File: the 23-LDMK deform_map file
2) File Type: Metric
3) Flat Max Edge Length: 10.00
4) Metric Deformation: Nearest Node (not sure which one is better?)
5) Smooth One Iteration (Except Flat)

The other buttons were not clickable (the dialog box does not allow me to
use them).

When I click the "Apply" button, I immediately receive the following error
message:

Deform Error
Is deformation map file valid? You must select a data file for
deformation. You must select the output name for the deformed file.

I tried to apply deformation map from two different .spec files:

1) Macaque F99 atlas directory, which has deformed metric files (from
individual macaque to F99). I added/appended the .deform_map file to this
.spec file before applying deformation.

2) COMPARE_MACAQUE_HUMAN directory (as a part of CARET_TUTORIAL_SEPT06
directory). I added/appended my metric files to this .spec file before
applying deformation.

In both cases, I got the same error.


Thanks for your helpful comments/suggestions,

Reza


  

Reza,

On Mar 10, 2007, at 9:31 PM, Reza Rajimehr wrote:



Dear caret-users,

David Van Essen suggested me to use the following .deform_map file for
deformation of macaque F99 to Human PALS:

RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-
LDMK-VE.73730.spec.deform_map
  

Once you have a deform_map file, you can use it to register data
sets  from monkey to human WITHOUT re-running a registration.  This
is done using the Surface: Deformation: Apply Deformation Map
option.  If you want to register paint files, metric files, and most
other files, you don't need anything other than the deform_map file
to get the job done, and the dialog window is fairly self-
explanatory.  If you want to register a border projection file or a
coordinate file, then you need additional coordinate and topology
files that are available as part of the Caret Sept_06 tutorial dataset:
http://sumsdb.wustl.edu/sums/archivelist.do?
archive_id=6595051&archive_name=COMPARE_PALS_MacaqueF99.73730.spec

The only reason to actually re-run an interspecies registration is IF
you don't like the particular set of landmarks used and you want to
try your own.  If so, you should start with borderproj files also in:
http://sumsdb.wustl.edu/sums/archivelist.do?
archive_id=6595051&archive_name=COMPARE_PALS_MacaqueF99.73730.spec
and make your additions and subtractions from there.

See Part 4 of the latest Caret tutorial for more details on monkey-
human comparisons.
http://sumsdb.wustl.edu/sums/directory.do?
id=6585200&dir_name=CARET_TUTORIAL_SEPT-06



I specified this as my .deform_map file in the Spherical Parameters
tab in
the Spherical Surface Deformation dialog box. My question is what I
should
specify as .borderproj file. I have a borderproj file in my F99
directory
(that I used for the registration of individual macaque to F99). I
also
have a borderproj file in my PALS directory (that I used for the
registration of individual human to PALS). Should I use these
borderproj
files in the Individual and Atlas tabs in the Spherical Surface
Deformation dia

Re: [caret-users] About Monkey to Human Deformation

[Reza Rajimehr]

Dear David,

In the "Apply Deformation Map" dialog box, I specified the following items:

1) Deformation Map File: the 23-LDMK deform_map file
2) File Type: Metric
3) Flat Max Edge Length: 10.00
4) Metric Deformation: Nearest Node (not sure which one is better?)
5) Smooth One Iteration (Except Flat)

The other buttons were not clickable (the dialog box does not allow me to
use them).

When I click the "Apply" button, I immediately receive the following error
message:

Deform Error
Is deformation map file valid? You must select a data file for
deformation. You must select the output name for the deformed file.

I tried to apply deformation map from two different .spec files:

1) Macaque F99 atlas directory, which has deformed metric files (from
individual macaque to F99). I added/appended the .deform_map file to this
.spec file before applying deformation.

2) COMPARE_MACAQUE_HUMAN directory (as a part of CARET_TUTORIAL_SEPT06
directory). I added/appended my metric files to this .spec file before
applying deformation.

In both cases, I got the same error.


Thanks for your helpful comments/suggestions,

Reza


> Reza,
>
> On Mar 10, 2007, at 9:31 PM, Reza Rajimehr wrote:
>
>> Dear caret-users,
>>
>> David Van Essen suggested me to use the following .deform_map file for
>> deformation of macaque F99 to Human PALS:
>>
>> RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-
>> LDMK-VE.73730.spec.deform_map
>
> Once you have a deform_map file, you can use it to register data
> sets  from monkey to human WITHOUT re-running a registration.  This
> is done using the Surface: Deformation: Apply Deformation Map
> option.  If you want to register paint files, metric files, and most
> other files, you don't need anything other than the deform_map file
> to get the job done, and the dialog window is fairly self-
> explanatory.  If you want to register a border projection file or a
> coordinate file, then you need additional coordinate and topology
> files that are available as part of the Caret Sept_06 tutorial dataset:
> http://sumsdb.wustl.edu/sums/archivelist.do?
> archive_id=6595051&archive_name=COMPARE_PALS_MacaqueF99.73730.spec
>
> The only reason to actually re-run an interspecies registration is IF
> you don't like the particular set of landmarks used and you want to
> try your own.  If so, you should start with borderproj files also in:
> http://sumsdb.wustl.edu/sums/archivelist.do?
> archive_id=6595051&archive_name=COMPARE_PALS_MacaqueF99.73730.spec
> and make your additions and subtractions from there.
>
> See Part 4 of the latest Caret tutorial for more details on monkey-
> human comparisons.
> http://sumsdb.wustl.edu/sums/directory.do?
> id=6585200&dir_name=CARET_TUTORIAL_SEPT-06
>
>>
>> I specified this as my .deform_map file in the Spherical Parameters
>> tab in
>> the Spherical Surface Deformation dialog box. My question is what I
>> should
>> specify as .borderproj file. I have a borderproj file in my F99
>> directory
>> (that I used for the registration of individual macaque to F99). I
>> also
>> have a borderproj file in my PALS directory (that I used for the
>> registration of individual human to PALS). Should I use these
>> borderproj
>> files in the Individual and Atlas tabs in the Spherical Surface
>> Deformation dialog box? Or there are other files that I should use?
>>
>> I also assume that the macaque F99 .spec file should be used in the
>> Individual tab, and the human PALS .spec file should be used in the
>> Atlas
>> tab.
>
> See above.  These steps should not be necessary for your purposes.
>
> I hope this helps.
>
> David
>
>>
>> Thanks for your help,
>> Reza
>>
>> 
>> Reza Rajimehr, MD
>>
>> NMR Athinoula A. Martinos Center
>> Department of Radiology
>> Massachusetts General Hospital (MGH)
>> Building 149, 13th St.
>> Charlestown, MA 02129
>>
>> Email: [EMAIL PROTECTED]
>> 
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>
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Reza Rajimehr, MD

NMR Athinoula A. Martinos Center
Department of Radiology
Massachusetts General Hospital (MGH)
Building 149, 13th St.
Charlestown, MA 02129

Email: [EMAIL PROTECTED]

Re: [caret-users] the name

[Ervin Berényi]

Thank's Donna!

On 13/03/07, Donna Dierker <[EMAIL PROTECTED]> wrote:


Hi Ervin,

I think the confusion stemmed from receiving a caret-users mailing list
confirmation with a more personalized login and password around the same
time you receive the download information.  To download Caret, use this
access information:

> To obtain the Caret software, use this login ID and password
>  login: Rabbit
>  password: Carrot
Donna

The Caret software can be downloaded from
"http://brainmap.wustl.edu/caret#DownloadCaret";.

On 03/13/2007 08:01 AM, Ervin Berényi wrote:
> What is my "name"?
>
> The password is correct.
>
> I can't login to the downloading area.
>
> Ervin Berényi
> 

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