subject:"Re\: \[caret\-users\] using caret for a meta\-analysis"

RE: [caret-users] using caret for a meta-analysis

2007-01-08 Thread Leon Deouell

That seems to do the trick. Thanks. 

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of David Vanessen
Sent: Sunday, January 07, 2007 7:30 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

Leon,

I can replicate and explain your observations in the following way:

1) Load a foci file that contains data in multiple stereotaxic  
spaces, and view the foci with the FLIRT average fiducial surface in  
the main window..  At this stage, each focus will be in its original  
space, even though you are viewing the FLIRT average fiducial surface.

2) Open a second Caret window that contains a non-fiducial surface  
(e.g., the inflated surface).  Note that no foci are visible on the  
inflated surface prior to projection.

3) Apply Layers: Foci: Project Foci to PALS atlas.  As the projection  
process occurs, each focus that didn't start out as already being in  
FLIRT space will jump to a new position, by an amount that reflects  
the difference between FLIRT and whatever space the focus originated  
in.  Concurrently, foci will start appearing on the inflated  
surface.  Once the projection process is completed, each focus should  
be visible only once on the fiducial surface.

4) Open the original foci file (using Open File or using Toolbar:  
Spec) and Append it to the current foci.  Now you should see most  
(but perhaps not all) foci doubled in the average fiducial surface  
view but not in the inflated view.

In other words, I infer that you inadvertently loaded both the foci  
and the foci projection file to create the view in your email.  In  
general, you will want to avoid such quasi-duplication.  Instead,  
only view foci projection data once the projection is complete,  
unless you have a specific need to see the foci in their original space.

I hope this resolves your question.

David

On Jan 7, 2007, at 3:37 AM, Leon Deouell wrote:

> Hi,
>
> I am displaying my foci now(post projection to PALS-B12) on the  
> FIDUCIAL
> Human.PALS_B12.LEFT_AVG_B1-12.FIDICUAL_FLIRT.clean.73730.coord. For  
> some
> reason, it looks like every  blob is doubled (see window capture  
> attached).
> I don't see this if I display the same foci on the inflated or  
> hyperinflated
> brains. Any idea why this is happening?
>
> Thanks,
>
> Leon
>
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Donna  
> Dierker
> Sent: Friday, December 22, 2006 5:17 PM
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-users] using caret for a meta-analysis
>
> Thank YOU for figuring out your own problem -- a pretty obscure  
> one, at
> that.
>
> I agree both minus and long dash should read as minus; I hope it's not
> tough for John to do. Sometimes the I/O stuff is QT's domain and  
> not so
> easy to control.
>
> On 12/22/2006 09:05 AM, Leon Deouell wrote:
>> Dear Donna,
>>
>> Thanks to your critical eye, I found out what the problem is. You  
>> noted
> that
>> for focus 4 the description is L Superior Frontal Gyrus but the x
> coordinate
>> was 20 in your readout. However, in the foci file I've sent, the line
>> actually says:
>> 4,-20,23,51,,MolholmEtAl05.pitch,0,L superior frontal  
>> gyrusPure,,pitch
>>
>> I am not sure what you used to read the foci file, but it seems this
>> software, like CARET, ignored the minus sign, and it turns out  
>> that all
> the
>> numbers which were zeroed in CARET, where actually negative  
>> numbers in my
>> original foci file. I tracked the problem back to the character  
>> used for
> the
>> minus sign. When I created the excel file (from which I created  
>> the CSV
> foci
>> file), I have sometimes cut and paste from PDF files or HTML files  
>> of the
>> original articles. In some cases, the minus sign was a longer dash  
>> sign
>> rather than a real minus sign. They look very similar but the wrong
>> character is a slightly longer line if you look at it carefully.  
>> If you
> open
>> the foci file I've sent before with Notepad (that is, if you use  
>> Windows)
>> you will see what I mean. When I replaced these characters with  
>> real minus
>> signs, the apparent bug was solved.
>>
>> I think this is a point to keep in mind because I am pretty sure many
> would
>> cut and paste when creating large meta-analysis files (I have more  
>> than
> 100
>> points in the full file) rather than retype (which is also more  
>> prone to
>> errors). Maybe CARET can be configured to detect this somehow and  
>> either
>> report the problem or ac

Re: [caret-users] using caret for a meta-analysis

2007-01-08 Thread Donna Dierker


Hi Leon,

Is it possible you have both a foci and fociproj file, both of which are 
loaded?


On 01/07/2007 03:37 AM, Leon Deouell wrote:

Hi,

I am displaying my foci now(post projection to PALS-B12) on the FIDUCIAL
Human.PALS_B12.LEFT_AVG_B1-12.FIDICUAL_FLIRT.clean.73730.coord. For some
reason, it looks like every  blob is doubled (see window capture attached).
I don't see this if I display the same foci on the inflated or hyperinflated
brains. Any idea why this is happening?

Thanks,

Leon

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 22, 2006 5:17 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

Thank YOU for figuring out your own problem -- a pretty obscure one, at 
that.


I agree both minus and long dash should read as minus; I hope it's not 
tough for John to do. Sometimes the I/O stuff is QT's domain and not so 
easy to control.


On 12/22/2006 09:05 AM, Leon Deouell wrote:
  

Dear Donna,

Thanks to your critical eye, I found out what the problem is. You noted


that
  

for focus 4 the description is L Superior Frontal Gyrus but the x


coordinate
  

was 20 in your readout. However, in the foci file I've sent, the line
actually says: 
4,-20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch


I am not sure what you used to read the foci file, but it seems this
software, like CARET, ignored the minus sign, and it turns out that all


the
  

numbers which were zeroed in CARET, where actually negative numbers in my
original foci file. I tracked the problem back to the character used for


the
  

minus sign. When I created the excel file (from which I created the CSV


foci
  

file), I have sometimes cut and paste from PDF files or HTML files of the
original articles. In some cases, the minus sign was a longer dash sign
rather than a real minus sign. They look very similar but the wrong
character is a slightly longer line if you look at it carefully. If you


open
  

the foci file I've sent before with Notepad (that is, if you use Windows)
you will see what I mean. When I replaced these characters with real minus
signs, the apparent bug was solved. 


I think this is a point to keep in mind because I am pretty sure many


would
  

cut and paste when creating large meta-analysis files (I have more than


100
  

points in the full file) rather than retype (which is also more prone to
errors). Maybe CARET can be configured to detect this somehow and either
report the problem or accept this other dash sign as minus. 

Many thanks for the quick response. 


Leon

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 22, 2006 4:19 PM
To: Leon Deouell
Cc: 'Caret, SureFit,and SuMS software users'
Subject: Re: [caret-users] using caret for a meta-analysis

Hi Leon,

This looks like a bug to me.  I was able to replicate this behavior on 
my Caret 5.502 12/15/2006 Caret running RHEL.  The ID readout for these 
foci were just fine (readout followed by corresponding line from foci


file):
  

Focus 2: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0)
2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch

Focus 3: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0)
3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal gyrusPure,,pitch

But these foci had their x or y coordinate component zeroed out:

Focus 4: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0)
4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch
[Note from Donna: If left SFG, then wouldn't it be -20?)

Focus 5: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0)
5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal


lobulePure,,pitch
  

Focus 6: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0)
6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital gyrusPure,,pitch

On 12/22/2006 03:26 AM, Leon Deouell wrote:
  


Hi,

I am finding something peculiar when looking at foci. To illustrate, I
created a smaller file with only one study (foci file attached). I went
through the following steps:

1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the
/CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder
2. Opened the foci file test1study.foci
3. Projected the foci using Layers/Foci/Project Foci to PALS atlas
(selecting 'project above surface [0.00]).

The projected foci can be viewed in the attached figure coordinates.jpg

Now I click on foci, and look the Identify Window. I find that for some,

  

the
  


values in 'Original

Re: [caret-users] using caret for a meta-analysis

2007-01-07 Thread David Vanessen


Leon,

I can replicate and explain your observations in the following way:

1) Load a foci file that contains data in multiple stereotaxic  
spaces, and view the foci with the FLIRT average fiducial surface in  
the main window..  At this stage, each focus will be in its original  
space, even though you are viewing the FLIRT average fiducial surface.


2) Open a second Caret window that contains a non-fiducial surface  
(e.g., the inflated surface).  Note that no foci are visible on the  
inflated surface prior to projection.


3) Apply Layers: Foci: Project Foci to PALS atlas.  As the projection  
process occurs, each focus that didn't start out as already being in  
FLIRT space will jump to a new position, by an amount that reflects  
the difference between FLIRT and whatever space the focus originated  
in.  Concurrently, foci will start appearing on the inflated  
surface.  Once the projection process is completed, each focus should  
be visible only once on the fiducial surface.


4) Open the original foci file (using Open File or using Toolbar:  
Spec) and Append it to the current foci.  Now you should see most  
(but perhaps not all) foci doubled in the average fiducial surface  
view but not in the inflated view.


In other words, I infer that you inadvertently loaded both the foci  
and the foci projection file to create the view in your email.  In  
general, you will want to avoid such quasi-duplication.  Instead,  
only view foci projection data once the projection is complete,  
unless you have a specific need to see the foci in their original space.


I hope this resolves your question.

David


On Jan 7, 2007, at 3:37 AM, Leon Deouell wrote:


Hi,

I am displaying my foci now(post projection to PALS-B12) on the  
FIDUCIAL
Human.PALS_B12.LEFT_AVG_B1-12.FIDICUAL_FLIRT.clean.73730.coord. For  
some
reason, it looks like every  blob is doubled (see window capture  
attached).
I don't see this if I display the same foci on the inflated or  
hyperinflated

brains. Any idea why this is happening?

Thanks,

Leon

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna  
Dierker

Sent: Friday, December 22, 2006 5:17 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

Thank YOU for figuring out your own problem -- a pretty obscure  
one, at

that.

I agree both minus and long dash should read as minus; I hope it's not
tough for John to do. Sometimes the I/O stuff is QT's domain and  
not so

easy to control.

On 12/22/2006 09:05 AM, Leon Deouell wrote:

Dear Donna,

Thanks to your critical eye, I found out what the problem is. You  
noted

that

for focus 4 the description is L Superior Frontal Gyrus but the x

coordinate

was 20 in your readout. However, in the foci file I've sent, the line
actually says:
4,-20,23,51,,MolholmEtAl05.pitch,0,L superior frontal  
gyrusPure,,pitch


I am not sure what you used to read the foci file, but it seems this
software, like CARET, ignored the minus sign, and it turns out  
that all

the
numbers which were zeroed in CARET, where actually negative  
numbers in my
original foci file. I tracked the problem back to the character  
used for

the
minus sign. When I created the excel file (from which I created  
the CSV

foci
file), I have sometimes cut and paste from PDF files or HTML files  
of the
original articles. In some cases, the minus sign was a longer dash  
sign

rather than a real minus sign. They look very similar but the wrong
character is a slightly longer line if you look at it carefully.  
If you

open
the foci file I've sent before with Notepad (that is, if you use  
Windows)
you will see what I mean. When I replaced these characters with  
real minus

signs, the apparent bug was solved.

I think this is a point to keep in mind because I am pretty sure many

would
cut and paste when creating large meta-analysis files (I have more  
than

100
points in the full file) rather than retype (which is also more  
prone to
errors). Maybe CARET can be configured to detect this somehow and  
either

report the problem or accept this other dash sign as minus.

Many thanks for the quick response.

Leon

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna  
Dierker

Sent: Friday, December 22, 2006 4:19 PM
To: Leon Deouell
Cc: 'Caret, SureFit,and SuMS software users'
Subject: Re: [caret-users] using caret for a meta-analysis

Hi Leon,

This looks like a bug to me.  I was able to replicate this  
behavior on
my Caret 5.502 12/15/2006 Caret running RHEL.  The ID readout for  
these

foci were just fine (readout followed by corresponding line from foci

file):


Focus 2: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0)
2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal  
gyrusPure,,pitch


Focus 3: MolholmEtAl05.pitch   Class: pitch
Ori

RE: [caret-users] using caret for a meta-analysis

2007-01-07 Thread Leon Deouell

Hi,

I am displaying my foci now(post projection to PALS-B12) on the FIDUCIAL
Human.PALS_B12.LEFT_AVG_B1-12.FIDICUAL_FLIRT.clean.73730.coord. For some
reason, it looks like every  blob is doubled (see window capture attached).
I don't see this if I display the same foci on the inflated or hyperinflated
brains. Any idea why this is happening?

Thanks,

Leon

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 22, 2006 5:17 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

Thank YOU for figuring out your own problem -- a pretty obscure one, at 
that.

I agree both minus and long dash should read as minus; I hope it's not 
tough for John to do. Sometimes the I/O stuff is QT's domain and not so 
easy to control.

On 12/22/2006 09:05 AM, Leon Deouell wrote:
> Dear Donna,
>
> Thanks to your critical eye, I found out what the problem is. You noted
that
> for focus 4 the description is L Superior Frontal Gyrus but the x
coordinate
> was 20 in your readout. However, in the foci file I've sent, the line
> actually says: 
> 4,-20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch
>
> I am not sure what you used to read the foci file, but it seems this
> software, like CARET, ignored the minus sign, and it turns out that all
the
> numbers which were zeroed in CARET, where actually negative numbers in my
> original foci file. I tracked the problem back to the character used for
the
> minus sign. When I created the excel file (from which I created the CSV
foci
> file), I have sometimes cut and paste from PDF files or HTML files of the
> original articles. In some cases, the minus sign was a longer dash sign
> rather than a real minus sign. They look very similar but the wrong
> character is a slightly longer line if you look at it carefully. If you
open
> the foci file I've sent before with Notepad (that is, if you use Windows)
> you will see what I mean. When I replaced these characters with real minus
> signs, the apparent bug was solved. 
>
> I think this is a point to keep in mind because I am pretty sure many
would
> cut and paste when creating large meta-analysis files (I have more than
100
> points in the full file) rather than retype (which is also more prone to
> errors). Maybe CARET can be configured to detect this somehow and either
> report the problem or accept this other dash sign as minus. 
>
> Many thanks for the quick response. 
>
> Leon
>
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
> Sent: Friday, December 22, 2006 4:19 PM
> To: Leon Deouell
> Cc: 'Caret, SureFit,and SuMS software users'
> Subject: Re: [caret-users] using caret for a meta-analysis
>
> Hi Leon,
>
> This looks like a bug to me.  I was able to replicate this behavior on 
> my Caret 5.502 12/15/2006 Caret running RHEL.  The ID readout for these 
> foci were just fine (readout followed by corresponding line from foci
file):
>
> Focus 2: MolholmEtAl05.pitch   Class: pitch
> Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0)
> 2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch
>
> Focus 3: MolholmEtAl05.pitch   Class: pitch
> Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0)
> 3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal gyrusPure,,pitch
>
> But these foci had their x or y coordinate component zeroed out:
>
> Focus 4: MolholmEtAl05.pitch   Class: pitch
> Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0)
> 4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch
> [Note from Donna: If left SFG, then wouldn't it be -20?)
>
> Focus 5: MolholmEtAl05.pitch   Class: pitch
> Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0)
> 5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal
lobulePure,,pitch
>
> Focus 6: MolholmEtAl05.pitch   Class: pitch
> Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0)
> 6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital gyrusPure,,pitch
>
> On 12/22/2006 03:26 AM, Leon Deouell wrote:
>   
>> Hi,
>>
>> I am finding something peculiar when looking at foci. To illustrate, I
>> created a smaller file with only one study (foci file attached). I went
>> through the following steps:
>>
>> 1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the
>> /CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder
>> 2. Opened the foci file test1study.foci
>> 3. Projected the foci using Layers/Foci/Project Foci to PALS atlas
>> (selecting 'project above surface [0.00]).
>>
>> The pro

Re: [caret-users] using caret for a meta-analysis

2006-12-22 Thread John Harwell



Hello,

I have modified Caret to look for these unicode dashes (em-dash, en- 
dash, etc) that range from 8208 to 8213 when reading a comma  
separated file.  In addition, Caret will now print a message if an  
invalid character is found in text representations of floating point  
numbers.


John Harwell

On Dec 22, 2006, at 9:16 AM, Leon Deouell wrote:

Ps. In case this helps any: This is the wrong characther: '-', and  
this is
the right one: '-' . Using abs('-') in Matlab, the wrong one  
translates to

8211, while the correct minus sign translates to 45.

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna  
Dierker

Sent: Friday, December 22, 2006 4:19 PM
To: Leon Deouell
Cc: 'Caret, SureFit,and SuMS software users'
Subject: Re: [caret-users] using caret for a meta-analysis

Hi Leon,

This looks like a bug to me.  I was able to replicate this behavior on
my Caret 5.502 12/15/2006 Caret running RHEL.  The ID readout for  
these
foci were just fine (readout followed by corresponding line from  
foci file):


Focus 2: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0)
2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch

Focus 3: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0)
3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal  
gyrusPure,,pitch


But these foci had their x or y coordinate component zeroed out:

Focus 4: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0)
4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal  
gyrusPure,,pitch

[Note from Donna: If left SFG, then wouldn't it be -20?)

Focus 5: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0)
5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal  
lobulePure,,pitch


Focus 6: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0)
6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital  
gyrusPure,,pitch


On 12/22/2006 03:26 AM, Leon Deouell wrote:

Hi,

I am finding something peculiar when looking at foci. To  
illustrate, I
created a smaller file with only one study (foci file attached). I  
went

through the following steps:

1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec  
from the

/CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder
2. Opened the foci file test1study.foci
3. Projected the foci using Layers/Foci/Project Foci to PALS atlas
(selecting 'project above surface [0.00]).

The projected foci can be viewed in the attached figure  
coordinates.jpg


Now I click on foci, and look the Identify Window. I find that for  
some,

the
values in 'Original Sterotaxic Positions' match the coordinates in  
the

foci
file. But for some (e.g., the one marked with a red ellipse in the  
figure)

I
get one of the coordinates set to zero. For example for this  
focus, I get:


_
Focus 6: MolholmEtAl05.pitch  Class: pitch
 Original Stereotaxic Position (AFNI): 41.0 0.0 6.0
 Stereotaxic Position (FLIRT):  41.0 0.9 2.1
_

But focus 6 coordinates as specified in the foci file are
actually [41, -75, 6]

The same happens to a few others (but not all) foci. Sometimes it  
is the y

coordinate that becomes zero, and sometimes the x coordinate.

I verified that it is not something to do with the foci projection  
- the

same results are obtained if I click the foci before projection.

Any idea what I may be doing wrong, or not interpreting correctly?

Thanks,

Leon







-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna  
Dierker

Sent: Friday, December 08, 2006 7:49 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

On 12/08/2006 11:44 AM, Leon Deouell wrote:


Dear Donna,

Thanks for the information. I realize the issue of different  
coordinate
spaces. What I am not sure of is this: If I specify the original  
space
(e.g., T88 or SPM2) for each study in the foci text file, or in  
the study
tab when entering individual foci using the GUI (5.2.2 in the  
tutorial),

will Caret take this into consideration when projecting to the PALS

brain?




Yes

Or do I have to go through some intermediate of transforming from  
one



space


to another? Originally I was considering using the tal2mni Matlab

function
from the Cambridge imagers web site you mentioned to get all  
coordinates

into MNI space, but maybe this is redundant in Caret.


The idea is to make this unnecessary -- as long as the stereotaxic  
space

in question is well-represented by one of these:

711-2C
AFNI
FLIRT
MRITOTAL
SPM2
SPM95
SPM96
SPM99


Thanks,

Leon

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTE

Re: [caret-users] using caret for a meta-analysis

2006-12-22 Thread Donna Dierker

Thank YOU for figuring out your own problem -- a pretty obscure one, at 
that.


I agree both minus and long dash should read as minus; I hope it's not 
tough for John to do. Sometimes the I/O stuff is QT's domain and not so 
easy to control.


On 12/22/2006 09:05 AM, Leon Deouell wrote:

Dear Donna,

Thanks to your critical eye, I found out what the problem is. You noted that
for focus 4 the description is L Superior Frontal Gyrus but the x coordinate
was 20 in your readout. However, in the foci file I've sent, the line
actually says: 
4,-20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch


I am not sure what you used to read the foci file, but it seems this
software, like CARET, ignored the minus sign, and it turns out that all the
numbers which were zeroed in CARET, where actually negative numbers in my
original foci file. I tracked the problem back to the character used for the
minus sign. When I created the excel file (from which I created the CSV foci
file), I have sometimes cut and paste from PDF files or HTML files of the
original articles. In some cases, the minus sign was a longer dash sign
rather than a real minus sign. They look very similar but the wrong
character is a slightly longer line if you look at it carefully. If you open
the foci file I've sent before with Notepad (that is, if you use Windows)
you will see what I mean. When I replaced these characters with real minus
signs, the apparent bug was solved. 


I think this is a point to keep in mind because I am pretty sure many would
cut and paste when creating large meta-analysis files (I have more than 100
points in the full file) rather than retype (which is also more prone to
errors). Maybe CARET can be configured to detect this somehow and either
report the problem or accept this other dash sign as minus. 

Many thanks for the quick response. 


Leon

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 22, 2006 4:19 PM
To: Leon Deouell
Cc: 'Caret, SureFit,and SuMS software users'
Subject: Re: [caret-users] using caret for a meta-analysis

Hi Leon,

This looks like a bug to me.  I was able to replicate this behavior on 
my Caret 5.502 12/15/2006 Caret running RHEL.  The ID readout for these 
foci were just fine (readout followed by corresponding line from foci file):


Focus 2: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0)
2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch

Focus 3: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0)
3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal gyrusPure,,pitch

But these foci had their x or y coordinate component zeroed out:

Focus 4: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0)
4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch
[Note from Donna: If left SFG, then wouldn't it be -20?)

Focus 5: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0)
5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal lobulePure,,pitch

Focus 6: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0)
6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital gyrusPure,,pitch

On 12/22/2006 03:26 AM, Leon Deouell wrote:
  

Hi,

I am finding something peculiar when looking at foci. To illustrate, I
created a smaller file with only one study (foci file attached). I went
through the following steps:

1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the
/CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder
2. Opened the foci file test1study.foci
3. Projected the foci using Layers/Foci/Project Foci to PALS atlas
(selecting 'project above surface [0.00]).

The projected foci can be viewed in the attached figure coordinates.jpg

Now I click on foci, and look the Identify Window. I find that for some,


the
  

values in 'Original Sterotaxic Positions' match the coordinates in the


foci
  

file. But for some (e.g., the one marked with a red ellipse in the figure)


I
  

get one of the coordinates set to zero. For example for this focus, I get:

_
Focus 6: MolholmEtAl05.pitch  Class: pitch
 Original Stereotaxic Position (AFNI): 41.0 0.0 6.0
 Stereotaxic Position (FLIRT):  41.0 0.9 2.1
_

But focus 6 coordinates as specified in the foci file are 
actually [41, -75, 6]


The same happens to a few others (but not all) foci. Sometimes it is the y
coordinate that becomes zero, and sometimes the x coordinate. 


I verified that it is not something to do with the foci projection - the
same results are obtained if I click the foci before projection. 


Any idea what I may be doing wr

RE: [caret-users] using caret for a meta-analysis

2006-12-22 Thread Leon Deouell

Ps. In case this helps any: This is the wrong characther: '-', and this is
the right one: '-' . Using abs('-') in Matlab, the wrong one translates to
8211, while the correct minus sign translates to 45.  

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 22, 2006 4:19 PM
To: Leon Deouell
Cc: 'Caret, SureFit,and SuMS software users'
Subject: Re: [caret-users] using caret for a meta-analysis

Hi Leon,

This looks like a bug to me.  I was able to replicate this behavior on 
my Caret 5.502 12/15/2006 Caret running RHEL.  The ID readout for these 
foci were just fine (readout followed by corresponding line from foci file):

Focus 2: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0)
2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch

Focus 3: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0)
3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal gyrusPure,,pitch

But these foci had their x or y coordinate component zeroed out:

Focus 4: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0)
4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch
[Note from Donna: If left SFG, then wouldn't it be -20?)

Focus 5: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0)
5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal lobulePure,,pitch

Focus 6: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0)
6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital gyrusPure,,pitch

On 12/22/2006 03:26 AM, Leon Deouell wrote:
> Hi,
>
> I am finding something peculiar when looking at foci. To illustrate, I
> created a smaller file with only one study (foci file attached). I went
> through the following steps:
>
> 1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the
> /CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder
> 2. Opened the foci file test1study.foci
> 3. Projected the foci using Layers/Foci/Project Foci to PALS atlas
> (selecting 'project above surface [0.00]).
>
> The projected foci can be viewed in the attached figure coordinates.jpg
>
> Now I click on foci, and look the Identify Window. I find that for some,
the
> values in 'Original Sterotaxic Positions' match the coordinates in the
foci
> file. But for some (e.g., the one marked with a red ellipse in the figure)
I
> get one of the coordinates set to zero. For example for this focus, I get:
>
> _
> Focus 6: MolholmEtAl05.pitch  Class: pitch
>  Original Stereotaxic Position (AFNI): 41.0 0.0 6.0
>  Stereotaxic Position (FLIRT):  41.0 0.9 2.1
> _
>
> But focus 6 coordinates as specified in the foci file are 
> actually [41, -75, 6]
>
> The same happens to a few others (but not all) foci. Sometimes it is the y
> coordinate that becomes zero, and sometimes the x coordinate. 
>
> I verified that it is not something to do with the foci projection - the
> same results are obtained if I click the foci before projection. 
>
> Any idea what I may be doing wrong, or not interpreting correctly?
>
> Thanks,
>
> Leon
>
>
>
>
>
>
>
> -Original Message-----
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
> Sent: Friday, December 08, 2006 7:49 PM
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-users] using caret for a meta-analysis
>
> On 12/08/2006 11:44 AM, Leon Deouell wrote:
>   
>> Dear Donna,
>>
>> Thanks for the information. I realize the issue of different coordinate
>> spaces. What I am not sure of is this: If I specify the original space
>> (e.g., T88 or SPM2) for each study in the foci text file, or in the study
>> tab when entering individual foci using the GUI (5.2.2 in the tutorial),
>> will Caret take this into consideration when projecting to the PALS
brain?
>>   
>> 
> Yes
>   
>> Or do I have to go through some intermediate of transforming from one
>> 
> space
>   
>> to another? Originally I was considering using the tal2mni Matlab
function
>> from the Cambridge imagers web site you mentioned to get all coordinates
>> into MNI space, but maybe this is redundant in Caret.
>>   
>> 
> The idea is to make this unnecessary -- as long as the stereotaxic space 
> in question is well-represented by one of these:
>
> 711-2C
> AFNI
> FLIRT
> MRITOTAL
> SPM2
> SPM95
> SPM96
> SPM99
>   
>> Th

RE: [caret-users] using caret for a meta-analysis

2006-12-22 Thread Leon Deouell

Dear Donna,

Thanks to your critical eye, I found out what the problem is. You noted that
for focus 4 the description is L Superior Frontal Gyrus but the x coordinate
was 20 in your readout. However, in the foci file I've sent, the line
actually says: 
4,-20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch

I am not sure what you used to read the foci file, but it seems this
software, like CARET, ignored the minus sign, and it turns out that all the
numbers which were zeroed in CARET, where actually negative numbers in my
original foci file. I tracked the problem back to the character used for the
minus sign. When I created the excel file (from which I created the CSV foci
file), I have sometimes cut and paste from PDF files or HTML files of the
original articles. In some cases, the minus sign was a longer dash sign
rather than a real minus sign. They look very similar but the wrong
character is a slightly longer line if you look at it carefully. If you open
the foci file I've sent before with Notepad (that is, if you use Windows)
you will see what I mean. When I replaced these characters with real minus
signs, the apparent bug was solved. 

I think this is a point to keep in mind because I am pretty sure many would
cut and paste when creating large meta-analysis files (I have more than 100
points in the full file) rather than retype (which is also more prone to
errors). Maybe CARET can be configured to detect this somehow and either
report the problem or accept this other dash sign as minus. 

Many thanks for the quick response. 

Leon

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 22, 2006 4:19 PM
To: Leon Deouell
Cc: 'Caret, SureFit,and SuMS software users'
Subject: Re: [caret-users] using caret for a meta-analysis

Hi Leon,

This looks like a bug to me.  I was able to replicate this behavior on 
my Caret 5.502 12/15/2006 Caret running RHEL.  The ID readout for these 
foci were just fine (readout followed by corresponding line from foci file):

Focus 2: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0)
2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch

Focus 3: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0)
3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal gyrusPure,,pitch

But these foci had their x or y coordinate component zeroed out:

Focus 4: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0)
4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch
[Note from Donna: If left SFG, then wouldn't it be -20?)

Focus 5: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0)
5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal lobulePure,,pitch

Focus 6: MolholmEtAl05.pitch   Class: pitch
Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0)
6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital gyrusPure,,pitch

On 12/22/2006 03:26 AM, Leon Deouell wrote:
> Hi,
>
> I am finding something peculiar when looking at foci. To illustrate, I
> created a smaller file with only one study (foci file attached). I went
> through the following steps:
>
> 1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the
> /CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder
> 2. Opened the foci file test1study.foci
> 3. Projected the foci using Layers/Foci/Project Foci to PALS atlas
> (selecting 'project above surface [0.00]).
>
> The projected foci can be viewed in the attached figure coordinates.jpg
>
> Now I click on foci, and look the Identify Window. I find that for some,
the
> values in 'Original Sterotaxic Positions' match the coordinates in the
foci
> file. But for some (e.g., the one marked with a red ellipse in the figure)
I
> get one of the coordinates set to zero. For example for this focus, I get:
>
> _
> Focus 6: MolholmEtAl05.pitch  Class: pitch
>  Original Stereotaxic Position (AFNI): 41.0 0.0 6.0
>  Stereotaxic Position (FLIRT):  41.0 0.9 2.1
> _
>
> But focus 6 coordinates as specified in the foci file are 
> actually [41, -75, 6]
>
> The same happens to a few others (but not all) foci. Sometimes it is the y
> coordinate that becomes zero, and sometimes the x coordinate. 
>
> I verified that it is not something to do with the foci projection - the
> same results are obtained if I click the foci before projection. 
>
> Any idea what I may be doing wrong, or not interpreting correctly?
>
> Thanks,
>
> Leon
>
>
>
>
>
>
>
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTEC

Re: [caret-users] using caret for a meta-analysis

2006-12-22 Thread Donna Dierker


Hi Leon,

This looks like a bug to me.  I was able to replicate this behavior on 
my Caret 5.502 12/15/2006 Caret running RHEL.  The ID readout for these 
foci were just fine (readout followed by corresponding line from foci file):


Focus 2: MolholmEtAl05.pitch   Class: pitch
   Original Stereotaxic Position (AFNI): (42.0, 2.0, 53.0)
2,42,2,53,,MolholmEtAl05.pitch,0,R middle frontal gyrusPure,,pitch

Focus 3: MolholmEtAl05.pitch   Class: pitch
   Original Stereotaxic Position (AFNI): (52.0, 10.0, 18.0)
3,52,10,18,,MolholmEtAl05.pitch,0,R inferior frontal gyrusPure,,pitch

But these foci had their x or y coordinate component zeroed out:

Focus 4: MolholmEtAl05.pitch   Class: pitch
   Original Stereotaxic Position (AFNI): (0.0, 23.0, 51.0)
4,20,23,51,,MolholmEtAl05.pitch,0,L superior frontal gyrusPure,,pitch
[Note from Donna: If left SFG, then wouldn't it be -20?)

Focus 5: MolholmEtAl05.pitch   Class: pitch
   Original Stereotaxic Position (AFNI): (53.0, 0.0, 45.0)
5,53,38,45,,MolholmEtAl05.pitch,0,R inferior parietal lobulePure,,pitch

Focus 6: MolholmEtAl05.pitch   Class: pitch
   Original Stereotaxic Position (AFNI): (41.0, 0.0, 6.0)
6,41,75,6,,MolholmEtAl05.pitch,0,R middle occipital gyrusPure,,pitch

On 12/22/2006 03:26 AM, Leon Deouell wrote:

Hi,

I am finding something peculiar when looking at foci. To illustrate, I
created a smaller file with only one study (foci file attached). I went
through the following steps:

1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the
/CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder
2. Opened the foci file test1study.foci
3. Projected the foci using Layers/Foci/Project Foci to PALS atlas
(selecting 'project above surface [0.00]).

The projected foci can be viewed in the attached figure coordinates.jpg

Now I click on foci, and look the Identify Window. I find that for some, the
values in 'Original Sterotaxic Positions' match the coordinates in the foci
file. But for some (e.g., the one marked with a red ellipse in the figure) I
get one of the coordinates set to zero. For example for this focus, I get:

_
Focus 6: MolholmEtAl05.pitch  Class: pitch
 Original Stereotaxic Position (AFNI): 41.0 0.0 6.0
 Stereotaxic Position (FLIRT):  41.0 0.9 2.1
_

But focus 6 coordinates as specified in the foci file are 
actually [41, -75, 6]


The same happens to a few others (but not all) foci. Sometimes it is the y
coordinate that becomes zero, and sometimes the x coordinate. 


I verified that it is not something to do with the foci projection - the
same results are obtained if I click the foci before projection. 


Any idea what I may be doing wrong, or not interpreting correctly?

Thanks,

Leon







-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 08, 2006 7:49 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

On 12/08/2006 11:44 AM, Leon Deouell wrote:
  

Dear Donna,

Thanks for the information. I realize the issue of different coordinate
spaces. What I am not sure of is this: If I specify the original space
(e.g., T88 or SPM2) for each study in the foci text file, or in the study
tab when entering individual foci using the GUI (5.2.2 in the tutorial),
will Caret take this into consideration when projecting to the PALS brain?
  


Yes
  

Or do I have to go through some intermediate of transforming from one


space
  

to another? Originally I was considering using the tal2mni Matlab function
from the Cambridge imagers web site you mentioned to get all coordinates
into MNI space, but maybe this is redundant in Caret.
  

The idea is to make this unnecessary -- as long as the stereotaxic space 
in question is well-represented by one of these:


711-2C
AFNI
FLIRT
MRITOTAL
SPM2
SPM95
SPM96
SPM99
  

Thanks,

Leon   


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 08, 2006 6:34 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

Hi Leon,

Shawn has done exactly what you want to do, so if anyone knows the 
pitfalls, he does. ;-)


Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2 
of this tutorial, if you haven't done so already:


CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200

This tutorial includes a spec file intended for this purpose. The ones 
in the Caret fmri_mapping directory are not really intended for use as 
"visualization" specs; rather, Caret uses them when mapping fMRI data 
onto PALS_B12. You can, however, use the average fiducial surfaces in 
that directory for your foci-related purposes. Note that studies report 
results in stereotactic spaces other than MNI

RE: [caret-users] using caret for a meta-analysis

2006-12-22 Thread Leon Deouell

Hi,

I am finding something peculiar when looking at foci. To illustrate, I
created a smaller file with only one study (foci file attached). I went
through the following steps:

1. Opened PALS_B12.BOTH.TEMPLATE-Map_STEREOTAXIC-FOCI.73730.spec from the
/CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES/ folder
2. Opened the foci file test1study.foci
3. Projected the foci using Layers/Foci/Project Foci to PALS atlas
(selecting 'project above surface [0.00]).

The projected foci can be viewed in the attached figure coordinates.jpg

Now I click on foci, and look the Identify Window. I find that for some, the
values in 'Original Sterotaxic Positions' match the coordinates in the foci
file. But for some (e.g., the one marked with a red ellipse in the figure) I
get one of the coordinates set to zero. For example for this focus, I get:

_
Focus 6: MolholmEtAl05.pitch  Class: pitch
 Original Stereotaxic Position (AFNI): 41.0 0.0 6.0
 Stereotaxic Position (FLIRT):  41.0 0.9 2.1
_

But focus 6 coordinates as specified in the foci file are 
actually [41, -75, 6]

The same happens to a few others (but not all) foci. Sometimes it is the y
coordinate that becomes zero, and sometimes the x coordinate. 

I verified that it is not something to do with the foci projection - the
same results are obtained if I click the foci before projection. 

Any idea what I may be doing wrong, or not interpreting correctly?

Thanks,

Leon







-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 08, 2006 7:49 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

On 12/08/2006 11:44 AM, Leon Deouell wrote:
> Dear Donna,
>
> Thanks for the information. I realize the issue of different coordinate
> spaces. What I am not sure of is this: If I specify the original space
> (e.g., T88 or SPM2) for each study in the foci text file, or in the study
> tab when entering individual foci using the GUI (5.2.2 in the tutorial),
> will Caret take this into consideration when projecting to the PALS brain?
>   
Yes
> Or do I have to go through some intermediate of transforming from one
space
> to another? Originally I was considering using the tal2mni Matlab function
> from the Cambridge imagers web site you mentioned to get all coordinates
> into MNI space, but maybe this is redundant in Caret.
>   
The idea is to make this unnecessary -- as long as the stereotaxic space 
in question is well-represented by one of these:

711-2C
AFNI
FLIRT
MRITOTAL
SPM2
SPM95
SPM96
SPM99
> Thanks,
>
> Leon   
>
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
> Sent: Friday, December 08, 2006 6:34 PM
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-users] using caret for a meta-analysis
>
> Hi Leon,
>
> Shawn has done exactly what you want to do, so if anyone knows the 
> pitfalls, he does. ;-)
>
> Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2 
> of this tutorial, if you haven't done so already:
>
> CARET_TUTORIAL_SEPT-06
> http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200
>
> This tutorial includes a spec file intended for this purpose. The ones 
> in the Caret fmri_mapping directory are not really intended for use as 
> "visualization" specs; rather, Caret uses them when mapping fMRI data 
> onto PALS_B12. You can, however, use the average fiducial surfaces in 
> that directory for your foci-related purposes. Note that studies report 
> results in stereotactic spaces other than MNI (e.g., AFNI users report 
> true Talairach-Tournoux (T88) coordinates, which differs significantly 
> from MNI -- see http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach; 
> wustl.edu researchers typically use "711-2*" space -- somewhere between 
> T88 and MNI). See 
> http://brainvis.wustl.edu/help/pals_volume_normalization/ for additional 
> details.
>
> Reading tutorial section 5.2 may clarify some of this, but you're likely 
> to have residual questions/confusion about these spaces.
>
> On 12/08/2006 10:24 AM, Christ, Shawn E. wrote:
>   
>> Hi Leon,
>>
>> I have been working with David, Donna, and John on utilizing Caret for 
>> precisely this purpose with respect to an ALE-type meta-analysis on 
>> deception that we have submitted for publication. You can download a 
>> copy of our spec file, etc. at 
>> http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996
>>
>> I've also uploaded a copy of my personal notes on how to transform 
>> foci using Caret. They can be found at 
>> http:

Re: [caret-users] using caret for a meta-analysis

2006-12-09 Thread David Vanessen


Leon,

On Dec 9, 2006, at 7:59 AM, Leon Deouell wrote:

Thanks again for your help. I am making nice progress. My questions  
now are:
1. Is it possible to see the foci on volume slices? It seems I can  
only see

them on surface files.


Yes - Use File: Open Data File: Open Foci File - Volumes (*.foci).   
This will open any valid foci file, and use whatever foci color file  
you have selected.


Then select Display Control: Page Selection: Foci and toggle Show  
Volume Foci on.


2. Regardless of foci, when I switch to 'oblique' in a window  
displaying a
volume, I loose the yoking option - clicking on the surface does  
not change
the display in the volume window and vice versa. Is there a way to  
tilt the

volume and remain "yoked"?


My observations:  Clicking on the surface does not move the cursor in  
the volume when viewing oblique slices, but it works for me in the  
reverse direction - clicking on the volume slice does highlight the  
corresponding node in the surface.


Getting it to go in the reverse direction would be useful.  Also, I  
just noticed that the surface slices don't display in the oblique  
volume slices even when selected using the O/L-Volume: Surface  
Outline option.   However, John Harwell has a fair amount on his  
platter right now, so I'm not sure when he'll be able to get to it.


David VE



Leon

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna  
Dierker

Sent: Friday, December 08, 2006 7:49 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

On 12/08/2006 11:44 AM, Leon Deouell wrote:

Dear Donna,

Thanks for the information. I realize the issue of different  
coordinate
spaces. What I am not sure of is this: If I specify the original  
space
(e.g., T88 or SPM2) for each study in the foci text file, or in  
the study
tab when entering individual foci using the GUI (5.2.2 in the  
tutorial),
will Caret take this into consideration when projecting to the  
PALS brain?



Yes

Or do I have to go through some intermediate of transforming from one

space
to another? Originally I was considering using the tal2mni Matlab  
function
from the Cambridge imagers web site you mentioned to get all  
coordinates

into MNI space, but maybe this is redundant in Caret.

The idea is to make this unnecessary -- as long as the stereotaxic  
space

in question is well-represented by one of these:

711-2C
AFNI
FLIRT
MRITOTAL
SPM2
SPM95
SPM96
SPM99

Thanks,

Leon

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna  
Dierker

Sent: Friday, December 08, 2006 6:34 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

Hi Leon,

Shawn has done exactly what you want to do, so if anyone knows the
pitfalls, he does. ;-)

Besides Shawn's useful notes, make sure you read sections 1.2.3  
and 5.2

of this tutorial, if you haven't done so already:

CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200

This tutorial includes a spec file intended for this purpose. The  
ones
in the Caret fmri_mapping directory are not really intended for  
use as

"visualization" specs; rather, Caret uses them when mapping fMRI data
onto PALS_B12. You can, however, use the average fiducial surfaces in
that directory for your foci-related purposes. Note that studies  
report
results in stereotactic spaces other than MNI (e.g., AFNI users  
report
true Talairach-Tournoux (T88) coordinates, which differs  
significantly
from MNI -- see http://imaging.mrc-cbu.cam.ac.uk/imaging/ 
MniTalairach;
wustl.edu researchers typically use "711-2*" space -- somewhere  
between

T88 and MNI). See
http://brainvis.wustl.edu/help/pals_volume_normalization/ for  
additional

details.

Reading tutorial section 5.2 may clarify some of this, but you're  
likely

to have residual questions/confusion about these spaces.

On 12/08/2006 10:24 AM, Christ, Shawn E. wrote:


Hi Leon,

I have been working with David, Donna, and John on utilizing  
Caret for

precisely this purpose with respect to an ALE-type meta-analysis on
deception that we have submitted for publication. You can download a
copy of our spec file, etc. at
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996

I've also uploaded a copy of my personal notes on how to transform
foci using Caret. They can be found at
http://www.shawnchrist.com/FociTransform.pdf

I hope this helps!

Best,

-Shawn

--

Shawn Christ, Ph.D.

Assistant Professor

Department of Psychological Sciences

University of Missouri-Columbia

210 McAlester Hall

Columbia, MO 65211

[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>

 



*From:* [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] *On Behalf Of *Leon
Deouell
*Sent:

RE: [caret-users] using caret for a meta-analysis

2006-12-09 Thread Leon Deouell

Thanks again for your help. I am making nice progress. My questions now are:
1. Is it possible to see the foci on volume slices? It seems I can only see
them on surface files.
2. Regardless of foci, when I switch to 'oblique' in a window displaying a
volume, I loose the yoking option - clicking on the surface does not change
the display in the volume window and vice versa. Is there a way to tilt the
volume and remain "yoked"?

Leon

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 08, 2006 7:49 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

On 12/08/2006 11:44 AM, Leon Deouell wrote:
> Dear Donna,
>
> Thanks for the information. I realize the issue of different coordinate
> spaces. What I am not sure of is this: If I specify the original space
> (e.g., T88 or SPM2) for each study in the foci text file, or in the study
> tab when entering individual foci using the GUI (5.2.2 in the tutorial),
> will Caret take this into consideration when projecting to the PALS brain?
>   
Yes
> Or do I have to go through some intermediate of transforming from one
space
> to another? Originally I was considering using the tal2mni Matlab function
> from the Cambridge imagers web site you mentioned to get all coordinates
> into MNI space, but maybe this is redundant in Caret.
>   
The idea is to make this unnecessary -- as long as the stereotaxic space 
in question is well-represented by one of these:

711-2C
AFNI
FLIRT
MRITOTAL
SPM2
SPM95
SPM96
SPM99
> Thanks,
>
> Leon   
>
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
> Sent: Friday, December 08, 2006 6:34 PM
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-users] using caret for a meta-analysis
>
> Hi Leon,
>
> Shawn has done exactly what you want to do, so if anyone knows the 
> pitfalls, he does. ;-)
>
> Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2 
> of this tutorial, if you haven't done so already:
>
> CARET_TUTORIAL_SEPT-06
> http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200
>
> This tutorial includes a spec file intended for this purpose. The ones 
> in the Caret fmri_mapping directory are not really intended for use as 
> "visualization" specs; rather, Caret uses them when mapping fMRI data 
> onto PALS_B12. You can, however, use the average fiducial surfaces in 
> that directory for your foci-related purposes. Note that studies report 
> results in stereotactic spaces other than MNI (e.g., AFNI users report 
> true Talairach-Tournoux (T88) coordinates, which differs significantly 
> from MNI -- see http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach; 
> wustl.edu researchers typically use "711-2*" space -- somewhere between 
> T88 and MNI). See 
> http://brainvis.wustl.edu/help/pals_volume_normalization/ for additional 
> details.
>
> Reading tutorial section 5.2 may clarify some of this, but you're likely 
> to have residual questions/confusion about these spaces.
>
> On 12/08/2006 10:24 AM, Christ, Shawn E. wrote:
>   
>> Hi Leon,
>>
>> I have been working with David, Donna, and John on utilizing Caret for 
>> precisely this purpose with respect to an ALE-type meta-analysis on 
>> deception that we have submitted for publication. You can download a 
>> copy of our spec file, etc. at 
>> http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996
>>
>> I've also uploaded a copy of my personal notes on how to transform 
>> foci using Caret. They can be found at 
>> http://www.shawnchrist.com/FociTransform.pdf
>>
>> I hope this helps!
>>
>> Best,
>>
>> -Shawn
>>
>> --
>>
>> Shawn Christ, Ph.D.
>>
>> Assistant Professor
>>
>> Department of Psychological Sciences
>>
>> University of Missouri-Columbia
>>
>> 210 McAlester Hall
>>
>> Columbia, MO 65211
>>
>> [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
>>
>> 
>>
>> *From:* [EMAIL PROTECTED] 
>> [mailto:[EMAIL PROTECTED] *On Behalf Of *Leon 
>> Deouell
>> *Sent:* Friday, December 08, 2006 9:50 AM
>> *To:* caret-users@brainvis.wustl.edu
>> *Subject:* [caret-users] using caret for a meta-analysis
>>
>> Hi,
>>
>> I am in the process of doing a meta-analysis of imaging data. I am a 
>> complete novice to Caret, but from a quick look it seems it's 
>> stereotaxic foci

Re: [caret-users] using caret for a meta-analysis

2006-12-08 Thread Donna Dierker


On 12/08/2006 11:44 AM, Leon Deouell wrote:

Dear Donna,

Thanks for the information. I realize the issue of different coordinate
spaces. What I am not sure of is this: If I specify the original space
(e.g., T88 or SPM2) for each study in the foci text file, or in the study
tab when entering individual foci using the GUI (5.2.2 in the tutorial),
will Caret take this into consideration when projecting to the PALS brain?
  

Yes

Or do I have to go through some intermediate of transforming from one space
to another? Originally I was considering using the tal2mni Matlab function
from the Cambridge imagers web site you mentioned to get all coordinates
into MNI space, but maybe this is redundant in Caret.
  
The idea is to make this unnecessary -- as long as the stereotaxic space 
in question is well-represented by one of these:


711-2C
AFNI
FLIRT
MRITOTAL
SPM2
SPM95
SPM96
SPM99

Thanks,

Leon   


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 08, 2006 6:34 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

Hi Leon,

Shawn has done exactly what you want to do, so if anyone knows the 
pitfalls, he does. ;-)


Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2 
of this tutorial, if you haven't done so already:


CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200

This tutorial includes a spec file intended for this purpose. The ones 
in the Caret fmri_mapping directory are not really intended for use as 
"visualization" specs; rather, Caret uses them when mapping fMRI data 
onto PALS_B12. You can, however, use the average fiducial surfaces in 
that directory for your foci-related purposes. Note that studies report 
results in stereotactic spaces other than MNI (e.g., AFNI users report 
true Talairach-Tournoux (T88) coordinates, which differs significantly 
from MNI -- see http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach; 
wustl.edu researchers typically use "711-2*" space -- somewhere between 
T88 and MNI). See 
http://brainvis.wustl.edu/help/pals_volume_normalization/ for additional 
details.


Reading tutorial section 5.2 may clarify some of this, but you're likely 
to have residual questions/confusion about these spaces.


On 12/08/2006 10:24 AM, Christ, Shawn E. wrote:
  

Hi Leon,

I have been working with David, Donna, and John on utilizing Caret for 
precisely this purpose with respect to an ALE-type meta-analysis on 
deception that we have submitted for publication. You can download a 
copy of our spec file, etc. at 
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996


I've also uploaded a copy of my personal notes on how to transform 
foci using Caret. They can be found at 
http://www.shawnchrist.com/FociTransform.pdf


I hope this helps!

Best,

-Shawn

--

Shawn Christ, Ph.D.

Assistant Professor

Department of Psychological Sciences

University of Missouri-Columbia

210 McAlester Hall

Columbia, MO 65211

[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>



*From:* [EMAIL PROTECTED] 
[mailto:[EMAIL PROTECTED] *On Behalf Of *Leon 
Deouell

*Sent:* Friday, December 08, 2006 9:50 AM
*To:* caret-users@brainvis.wustl.edu
*Subject:* [caret-users] using caret for a meta-analysis

Hi,

I am in the process of doing a meta-analysis of imaging data. I am a 
complete novice to Caret, but from a quick look it seems it's 
stereotaxic foci functions would be ideal to log the peak activity 
data from different studies. Eventually I would like to display 
symbols for each peak on a 3D brain rendering of some sort. Perhaps 
Naively, I thought I could load a template brain (open a spec file), 
add foci (assuming for a moment I have all coordinates in MNI space) 
using for example 'layers>foci>map stererotaxic focus', and see them 
pop-out on the brain. However, at first pass, I run into the following 
questions:


a) What brain (spec file) should I load from the fMRI_mapping folder? 
There are so many of them. Is there anywhere a text file describing 
what these different files are?


b) If I enter a focus with coordinates which happen to be under the 
surface by a few millimeters, they don't show up on the surface. Is 
there a way to project them to the surface or to make the brain 
'transparent'?


c) Once I have the foci entered, can I project them to an inflated 
brain, and if so, how?


Finally, I assume I am not the first to want to use Caret for this 
purpose - does someone have a 'recipe' for such a project or tips on 
what pitfalls to avoid?


Thanks,

Leon



Dr. Leon Y Deouell, MD, PhD

Department of Psychology

The Hebrew University of Jerusalem

Jerusalem 91905

Isra

RE: [caret-users] using caret for a meta-analysis

2006-12-08 Thread Leon Deouell

Dear Donna,

Thanks for the information. I realize the issue of different coordinate
spaces. What I am not sure of is this: If I specify the original space
(e.g., T88 or SPM2) for each study in the foci text file, or in the study
tab when entering individual foci using the GUI (5.2.2 in the tutorial),
will Caret take this into consideration when projecting to the PALS brain?
Or do I have to go through some intermediate of transforming from one space
to another? Originally I was considering using the tal2mni Matlab function
from the Cambridge imagers web site you mentioned to get all coordinates
into MNI space, but maybe this is redundant in Caret.

Thanks,

Leon   

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Friday, December 08, 2006 6:34 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] using caret for a meta-analysis

Hi Leon,

Shawn has done exactly what you want to do, so if anyone knows the 
pitfalls, he does. ;-)

Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2 
of this tutorial, if you haven't done so already:

CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200

This tutorial includes a spec file intended for this purpose. The ones 
in the Caret fmri_mapping directory are not really intended for use as 
"visualization" specs; rather, Caret uses them when mapping fMRI data 
onto PALS_B12. You can, however, use the average fiducial surfaces in 
that directory for your foci-related purposes. Note that studies report 
results in stereotactic spaces other than MNI (e.g., AFNI users report 
true Talairach-Tournoux (T88) coordinates, which differs significantly 
from MNI -- see http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach; 
wustl.edu researchers typically use "711-2*" space -- somewhere between 
T88 and MNI). See 
http://brainvis.wustl.edu/help/pals_volume_normalization/ for additional 
details.

Reading tutorial section 5.2 may clarify some of this, but you're likely 
to have residual questions/confusion about these spaces.

On 12/08/2006 10:24 AM, Christ, Shawn E. wrote:
>
> Hi Leon,
>
> I have been working with David, Donna, and John on utilizing Caret for 
> precisely this purpose with respect to an ALE-type meta-analysis on 
> deception that we have submitted for publication. You can download a 
> copy of our spec file, etc. at 
> http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996
>
> I've also uploaded a copy of my personal notes on how to transform 
> foci using Caret. They can be found at 
> http://www.shawnchrist.com/FociTransform.pdf
>
> I hope this helps!
>
> Best,
>
> -Shawn
>
> --
>
> Shawn Christ, Ph.D.
>
> Assistant Professor
>
> Department of Psychological Sciences
>
> University of Missouri-Columbia
>
> 210 McAlester Hall
>
> Columbia, MO 65211
>
> [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
>
> 
>
> *From:* [EMAIL PROTECTED] 
> [mailto:[EMAIL PROTECTED] *On Behalf Of *Leon 
> Deouell
> *Sent:* Friday, December 08, 2006 9:50 AM
> *To:* caret-users@brainvis.wustl.edu
> *Subject:* [caret-users] using caret for a meta-analysis
>
> Hi,
>
> I am in the process of doing a meta-analysis of imaging data. I am a 
> complete novice to Caret, but from a quick look it seems it's 
> stereotaxic foci functions would be ideal to log the peak activity 
> data from different studies. Eventually I would like to display 
> symbols for each peak on a 3D brain rendering of some sort. Perhaps 
> Naively, I thought I could load a template brain (open a spec file), 
> add foci (assuming for a moment I have all coordinates in MNI space) 
> using for example 'layers>foci>map stererotaxic focus', and see them 
> pop-out on the brain. However, at first pass, I run into the following 
> questions:
>
> a) What brain (spec file) should I load from the fMRI_mapping folder? 
> There are so many of them. Is there anywhere a text file describing 
> what these different files are?
>
> b) If I enter a focus with coordinates which happen to be under the 
> surface by a few millimeters, they don't show up on the surface. Is 
> there a way to project them to the surface or to make the brain 
> 'transparent'?
>
> c) Once I have the foci entered, can I project them to an inflated 
> brain, and if so, how?
>
> Finally, I assume I am not the first to want to use Caret for this 
> purpose - does someone have a 'recipe' for such a project or tips on 
> what pitfalls to avoid?
>
> Thanks,
>
> Leon
>

Re: [caret-users] using caret for a meta-analysis

2006-12-08 Thread Donna Dierker


Hi Leon,

Shawn has done exactly what you want to do, so if anyone knows the 
pitfalls, he does. ;-)


Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2 
of this tutorial, if you haven't done so already:


CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200

This tutorial includes a spec file intended for this purpose. The ones 
in the Caret fmri_mapping directory are not really intended for use as 
"visualization" specs; rather, Caret uses them when mapping fMRI data 
onto PALS_B12. You can, however, use the average fiducial surfaces in 
that directory for your foci-related purposes. Note that studies report 
results in stereotactic spaces other than MNI (e.g., AFNI users report 
true Talairach-Tournoux (T88) coordinates, which differs significantly 
from MNI -- see http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach; 
wustl.edu researchers typically use "711-2*" space -- somewhere between 
T88 and MNI). See 
http://brainvis.wustl.edu/help/pals_volume_normalization/ for additional 
details.


Reading tutorial section 5.2 may clarify some of this, but you're likely 
to have residual questions/confusion about these spaces.


On 12/08/2006 10:24 AM, Christ, Shawn E. wrote:


Hi Leon,

I have been working with David, Donna, and John on utilizing Caret for 
precisely this purpose with respect to an ALE-type meta-analysis on 
deception that we have submitted for publication. You can download a 
copy of our spec file, etc. at 
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996


I’ve also uploaded a copy of my personal notes on how to transform 
foci using Caret. They can be found at 
http://www.shawnchrist.com/FociTransform.pdf


I hope this helps!

Best,

-Shawn

--

Shawn Christ, Ph.D.

Assistant Professor

Department of Psychological Sciences

University of Missouri-Columbia

210 McAlester Hall

Columbia, MO 65211

[EMAIL PROTECTED] 



*From:* [EMAIL PROTECTED] 
[mailto:[EMAIL PROTECTED] *On Behalf Of *Leon 
Deouell

*Sent:* Friday, December 08, 2006 9:50 AM
*To:* caret-users@brainvis.wustl.edu
*Subject:* [caret-users] using caret for a meta-analysis

Hi,

I am in the process of doing a meta-analysis of imaging data. I am a 
complete novice to Caret, but from a quick look it seems it's 
stereotaxic foci functions would be ideal to log the peak activity 
data from different studies. Eventually I would like to display 
symbols for each peak on a 3D brain rendering of some sort. Perhaps 
Naively, I thought I could load a template brain (open a spec file), 
add foci (assuming for a moment I have all coordinates in MNI space) 
using for example 'layers>foci>map stererotaxic focus', and see them 
pop-out on the brain. However, at first pass, I run into the following 
questions:


a) What brain (spec file) should I load from the fMRI_mapping folder? 
There are so many of them. Is there anywhere a text file describing 
what these different files are?


b) If I enter a focus with coordinates which happen to be under the 
surface by a few millimeters, they don't show up on the surface. Is 
there a way to project them to the surface or to make the brain 
'transparent'?


c) Once I have the foci entered, can I project them to an inflated 
brain, and if so, how?


Finally, I assume I am not the first to want to use Caret for this 
purpose – does someone have a 'recipe' for such a project or tips on 
what pitfalls to avoid?


Thanks,

Leon



Dr. Leon Y Deouell, MD, PhD

Department of Psychology

The Hebrew University of Jerusalem

Jerusalem 91905

Israel

Tel: +972-2-5881739

Fax: +972-2-5825659

http://pissaro.soc.huji.ac.il/~leon/Lab 





___
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] using caret for a meta-analysis

2006-12-08 Thread Leon Deouell

Hi Shawn,

 

Just what I was hoping for. Many thanks. 

 

Best,

 

Leon

 

 

 

  _  

From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Christ, Shawn
E.
Sent: Friday, December 08, 2006 6:25 PM
To: caret-users@brainvis.wustl.edu
Subject: RE: [caret-users] using caret for a meta-analysis

 

Hi Leon,

 

I have been working with David, Donna, and John on utilizing Caret for
precisely this purpose with respect to an ALE-type meta-analysis on
deception that we have submitted for publication.  You can download a copy
of our spec file, etc. at
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996

 

I've also uploaded a copy of my personal notes on how to transform foci
using Caret.  They can be found at
http://www.shawnchrist.com/FociTransform.pdf

 

I hope this helps!

 

Best,

-Shawn

 

 

--

Shawn Christ, Ph.D.

Assistant Professor

Department of Psychological Sciences

University of Missouri-Columbia

210 McAlester Hall

Columbia, MO 65211

[EMAIL PROTECTED]

 

  _  

From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Leon Deouell
Sent: Friday, December 08, 2006 9:50 AM
To: caret-users@brainvis.wustl.edu
Subject: [caret-users] using caret for a meta-analysis

 

Hi,

I am in the process of doing a meta-analysis of imaging data. I am a
complete novice to Caret, but from a quick look it seems it's stereotaxic
foci functions would be ideal to log the peak activity data from different
studies. Eventually I would like to display symbols for each peak on a 3D
brain rendering of some sort. Perhaps Naively, I thought I could load a
template brain (open a spec file), add foci (assuming for a moment I have
all coordinates in MNI space) using for example 'layers>foci>map
stererotaxic focus', and see them pop-out on the brain. However, at first
pass, I run into the following questions:

a) What brain (spec file) should I load from the fMRI_mapping folder? There
are so many of them. Is there anywhere a text file describing what these
different files are?

b) If I enter a focus with coordinates which happen to be under the surface
by a few millimeters, they don't show up on the surface. Is there a way to
project them to the surface or to make the brain 'transparent'?

c) Once I have the foci entered, can I project them to an inflated brain,
and if so, how?

Finally, I assume I am not the first to want to use Caret for this purpose -
does someone have a 'recipe' for such a project or tips on what pitfalls to
avoid?

Thanks,

Leon



Dr. Leon Y Deouell, MD, PhD

Department of Psychology

The Hebrew University of Jerusalem

Jerusalem 91905

Israel

Tel: +972-2-5881739

Fax: +972-2-5825659

 http://pissaro.soc.huji.ac.il/~leon/Lab

RE: [caret-users] using caret for a meta-analysis

2006-12-08 Thread Christ, Shawn E.

Hi Leon,

 

I have been working with David, Donna, and John on utilizing Caret for
precisely this purpose with respect to an ALE-type meta-analysis on
deception that we have submitted for publication.  You can download a
copy of our spec file, etc. at
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996

 

I've also uploaded a copy of my personal notes on how to transform foci
using Caret.  They can be found at
http://www.shawnchrist.com/FociTransform.pdf

 

I hope this helps!

 

Best,

-Shawn

 

 

--

Shawn Christ, Ph.D.

Assistant Professor

Department of Psychological Sciences

University of Missouri-Columbia

210 McAlester Hall

Columbia, MO 65211

[EMAIL PROTECTED]

 



From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Leon
Deouell
Sent: Friday, December 08, 2006 9:50 AM
To: caret-users@brainvis.wustl.edu
Subject: [caret-users] using caret for a meta-analysis

 

Hi,

I am in the process of doing a meta-analysis of imaging data. I am a
complete novice to Caret, but from a quick look it seems it's
stereotaxic foci functions would be ideal to log the peak activity data
from different studies. Eventually I would like to display symbols for
each peak on a 3D brain rendering of some sort. Perhaps Naively, I
thought I could load a template brain (open a spec file), add foci
(assuming for a moment I have all coordinates in MNI space) using for
example 'layers>foci>map stererotaxic focus', and see them pop-out on
the brain. However, at first pass, I run into the following questions:

a) What brain (spec file) should I load from the fMRI_mapping folder?
There are so many of them. Is there anywhere a text file describing what
these different files are?

b) If I enter a focus with coordinates which happen to be under the
surface by a few millimeters, they don't show up on the surface. Is
there a way to project them to the surface or to make the brain
'transparent'?

c) Once I have the foci entered, can I project them to an inflated
brain, and if so, how?

Finally, I assume I am not the first to want to use Caret for this
purpose - does someone have a 'recipe' for such a project or tips on
what pitfalls to avoid?

Thanks,

Leon



Dr. Leon Y Deouell, MD, PhD

Department of Psychology

The Hebrew University of Jerusalem

Jerusalem 91905

Israel

Tel: +972-2-5881739

Fax: +972-2-5825659

 http://pissaro.soc.huji.ac.il/~leon/Lab

RE: [caret-users] using caret for a meta-analysis

Re: [caret-users] using caret for a meta-analysis

Re: [caret-users] using caret for a meta-analysis

RE: [caret-users] using caret for a meta-analysis

Re: [caret-users] using caret for a meta-analysis

Re: [caret-users] using caret for a meta-analysis

RE: [caret-users] using caret for a meta-analysis

RE: [caret-users] using caret for a meta-analysis

Re: [caret-users] using caret for a meta-analysis

RE: [caret-users] using caret for a meta-analysis

Re: [caret-users] using caret for a meta-analysis

RE: [caret-users] using caret for a meta-analysis

Re: [caret-users] using caret for a meta-analysis

RE: [caret-users] using caret for a meta-analysis

Re: [caret-users] using caret for a meta-analysis

RE: [caret-users] using caret for a meta-analysis

RE: [caret-users] using caret for a meta-analysis

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