Re: [BULK] Re: [caret-users] Map SPM volume

2007-03-08 Thread Donna Dierker 
 hem is in a different window. (For more details, take the full 
September 2006 tutorial 
http://sumsdb.wustl.edu/sums/directory.do?id=6585200.) I don't know of 
any plans to un-split the hemispheres (i.e., combine them into a 
single coord file). David seems to think of the hemispheres as mostly 
independent entities.


I'm sure you are not alone in your questions/concerns.

Donna

On 03/07/2007 04:39 PM, [EMAIL PROTECTED] wrote:

Thanks Donna, everything seems to work now, so I’m happy :)

About the surfaces, I saw something in the archive, is it a white brain,
or deflated pial:
http://sumsdb.wustl.edu:8081/sums/search.do?category_id=6
and then click the first option with a brain icon on it that is possible
to view in the web browser.

There are 12 versions of each hemisphere so I presume that it is an
individual brain. Do you think is ok to use one of them, or do you happen
to have an average surface?

I think you are right, inflated brains may be best suited for visualizing
purposes, however, just in case some stubborn SPM guy would like once in a
while see he’s activation the way he is used to….
I think Freesurfer has a pial surface. Maybe it works to import that somehow?

Also, it would be nice to have the option to see the whole brain at once
(the non-split way) even inflated, but I guess that’s not yet possible….

Cheers,
Julian


  

On 03/07/2007 10:27 AM, Julianm Macoveanu wrote:


Yes, I use the CARET_TUTORIAL_SEPT06/MAPPNING_PROCEDURES files, and load
the
Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec file.

I think I got the hang of it. The break through was, after creating the
metric file load one of the predefined scenes before trying to open my
metric file. In this way it didn't complain anymore about different
number
of nodes.

If I understand it right if I want now to see the activation on a pial
surface I should just open the coord file and add it to my template spec
file. Do you know where I could find this? I think it should also be
something between pial and fiducial.

  

The PALS_B12 atlas (and the colin atlas before it) has no pial
surfaces.  One can generate pseudo-pial surfaces by using Surface:
Geometry: Expand or Shrink surface to expand a fiducial surface, but
I've never tried this with an average fiducial surface, and I don't
really recommend it.  We prefer the inflated surface for visualization,
unless you have activity in the operculum or insula that is difficult to
see; in such cases, we then use the Very Inflated surface.  Activity in
buried sulci isn't visible when viewed on a pial or a regular fiducial
(less so with an average fiducial).

I realize some people still prefer looking at a highly structured pial
surface, but considering this is group data you're mapping, the
structure of any one individual is not really representative of the
group structure of your subjects.  We believe mapping to PALS_B12 and
viewing the results on the inflated surface is a more faithful
representation of your results than viewing them on, say, colin27's pial
surface.  Slowly, we're hoping to win you over. ;-)



Also, L and R are overlaid wrong, what SPM reports as left, I see it on
the
right hemisphere in Caret. How can this be changed?

  

Use File: Open Data File: volume functional file and check the Volume is
an SPM2 Volume with Right on Left checkbox.


Thanks,
Julian

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna
Dierker
Sent: Wednesday, March 07, 2007 4:05 PM
To: Caret, SureFit, and SuMS software users
Subject: [BULK] Re: [caret-users] Map SPM volume
Importance: Low

Hi Julian,

When mapping to atlas, are you selecting a spec file created from this
dataset:

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

... using steps as described in Section 5.1 of this tutorial:

Caret_Tutorial_Oct06.pdf
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379

It's tough to see how you could get this error under those
circumstances, since the files in that spec file (or derivative thereof)
all have the same 73730 standard mesh.

While this spec won't have a pial surface, it will have left and right
versions of the following configurations:

PALS_B12 average fiducial
inflated
very inflated
flat

Since you're using SPM2, I'd suggest replacing the average fiducial
coord files with these files:

Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord
Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord

To do so, after opening
Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec, select File:
Open Data File: and select
Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord.  Repeat
for Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord.
Then, select Toolbar: Spec and use the X buttons to delete these
versions, which are similar but not as optimal as the SPM2 versions in
your case:

Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord

RE: [BULK] Re: [caret-users] Map SPM volume

2007-03-07 Thread Julianm Macoveanu 
Yes, I use the CARET_TUTORIAL_SEPT06/MAPPNING_PROCEDURES files, and load the
Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec file.

I think I got the hang of it. The break through was, after creating the
metric file load one of the predefined scenes before trying to open my
metric file. In this way it didn't complain anymore about different number
of nodes.

If I understand it right if I want now to see the activation on a pial
surface I should just open the coord file and add it to my template spec
file. Do you know where I could find this? I think it should also be
something between pial and fiducial.

Also, L and R are overlaid wrong, what SPM reports as left, I see it on the
right hemisphere in Caret. How can this be changed?

Thanks,
Julian

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker
Sent: Wednesday, March 07, 2007 4:05 PM
To: Caret, SureFit, and SuMS software users
Subject: [BULK] Re: [caret-users] Map SPM volume
Importance: Low

Hi Julian,

When mapping to atlas, are you selecting a spec file created from this 
dataset:

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

... using steps as described in Section 5.1 of this tutorial:

Caret_Tutorial_Oct06.pdf
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379

It's tough to see how you could get this error under those 
circumstances, since the files in that spec file (or derivative thereof) 
all have the same 73730 standard mesh.

While this spec won't have a pial surface, it will have left and right 
versions of the following configurations:

PALS_B12 average fiducial
inflated
very inflated
flat

Since you're using SPM2, I'd suggest replacing the average fiducial 
coord files with these files:

Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord
Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord

To do so, after opening 
Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec, select File: 
Open Data File: and select 
Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord.  Repeat 
for Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord.  
Then, select Toolbar: Spec and use the X buttons to delete these 
versions, which are similar but not as optimal as the SPM2 versions in 
your case:

Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord
Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord

Both the SPM2 and FLIRT versions are in mni152 space, but the 
contributing PALS_B12 anatomicals were normalized using SPM2 for the 
SPM2 versions, while FSL's flirt (affine only) was used to normalize the 
FLIRT versions.

Donna

On 03/07/2007 08:33 AM, Julianm Macoveanu wrote:

 Hi guys,

 I need some help with basic stuff. I just want to use Caret to 
 visualize my SPM2 activations on inflated/Fiducial surfaces. So I have 
 the normalized volume file to start with.

  

 I have opened a spec file from the Caret tutorial, use the map volume 
 to surface function, choose my volume, then Map to spec file with 
 atlas (and without). I have also tried not to open any spec file to 
 begin with, and then just open the one I chose as output during the 
 mapping procedure

  

 As space I tried the SPM2, as this is the kind of volume I have (but 
 also 711-sc).

  

 After the metric file is generated, I just try to open it, but I get 
 the error that my metric file contains different number of nodes.

  

 What I would like to have is a spec file that have all different 
 surfaces (including pial and multi-fiducial which I could not find in 
 any examples of spec files) and then just create metric files from my 
 SPM volumes in order to visualize the activations.

  

 Cheers,

 Julian

  


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

Re: [BULK] Re: [caret-users] Map SPM volume

2007-03-07 Thread julianm 
Thanks Donna, everything seems to work now, so I’m happy :)

About the surfaces, I saw something in the archive, is it a white brain,
or deflated pial:
http://sumsdb.wustl.edu:8081/sums/search.do?category_id=6
and then click the first option with a brain icon on it that is possible
to view in the web browser.

There are 12 versions of each hemisphere so I presume that it is an
individual brain. Do you think is ok to use one of them, or do you happen
to have an average surface?

I think you are right, inflated brains may be best suited for visualizing
purposes, however, just in case some stubborn SPM guy would like once in a
while see he’s activation the way he is used to….
I think Freesurfer has a pial surface. Maybe it works to import that somehow?

Also, it would be nice to have the option to see the whole brain at once
(the non-split way) even inflated, but I guess that’s not yet possible….

Cheers,
Julian


 On 03/07/2007 10:27 AM, Julianm Macoveanu wrote:
 Yes, I use the CARET_TUTORIAL_SEPT06/MAPPNING_PROCEDURES files, and load
 the
 Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec file.

 I think I got the hang of it. The break through was, after creating the
 metric file load one of the predefined scenes before trying to open my
 metric file. In this way it didn't complain anymore about different
 number
 of nodes.

 If I understand it right if I want now to see the activation on a pial
 surface I should just open the coord file and add it to my template spec
 file. Do you know where I could find this? I think it should also be
 something between pial and fiducial.

 The PALS_B12 atlas (and the colin atlas before it) has no pial
 surfaces.  One can generate pseudo-pial surfaces by using Surface:
 Geometry: Expand or Shrink surface to expand a fiducial surface, but
 I've never tried this with an average fiducial surface, and I don't
 really recommend it.  We prefer the inflated surface for visualization,
 unless you have activity in the operculum or insula that is difficult to
 see; in such cases, we then use the Very Inflated surface.  Activity in
 buried sulci isn't visible when viewed on a pial or a regular fiducial
 (less so with an average fiducial).

 I realize some people still prefer looking at a highly structured pial
 surface, but considering this is group data you're mapping, the
 structure of any one individual is not really representative of the
 group structure of your subjects.  We believe mapping to PALS_B12 and
 viewing the results on the inflated surface is a more faithful
 representation of your results than viewing them on, say, colin27's pial
 surface.  Slowly, we're hoping to win you over. ;-)

 Also, L and R are overlaid wrong, what SPM reports as left, I see it on
 the
 right hemisphere in Caret. How can this be changed?

 Use File: Open Data File: volume functional file and check the Volume is
 an SPM2 Volume with Right on Left checkbox.
 Thanks,
 Julian

 -Original Message-
 From: [EMAIL PROTECTED]
 [mailto:[EMAIL PROTECTED] On Behalf Of Donna
 Dierker
 Sent: Wednesday, March 07, 2007 4:05 PM
 To: Caret, SureFit, and SuMS software users
 Subject: [BULK] Re: [caret-users] Map SPM volume
 Importance: Low

 Hi Julian,

 When mapping to atlas, are you selecting a spec file created from this
 dataset:

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

 ... using steps as described in Section 5.1 of this tutorial:

 Caret_Tutorial_Oct06.pdf
 http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379

 It's tough to see how you could get this error under those
 circumstances, since the files in that spec file (or derivative thereof)
 all have the same 73730 standard mesh.

 While this spec won't have a pial surface, it will have left and right
 versions of the following configurations:

 PALS_B12 average fiducial
 inflated
 very inflated
 flat

 Since you're using SPM2, I'd suggest replacing the average fiducial
 coord files with these files:

 Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord
 Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord

 To do so, after opening
 Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec, select File:
 Open Data File: and select
 Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord.  Repeat
 for Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord.
 Then, select Toolbar: Spec and use the X buttons to delete these
 versions, which are similar but not as optimal as the SPM2 versions in
 your case:

 Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord
 Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord

 Both the SPM2 and FLIRT versions are in mni152 space, but the
 contributing PALS_B12 anatomicals were normalized using SPM2 for the
 SPM2 versions, while FSL's flirt (affine only) was used to normalize the
 FLIRT versions.

 Donna

 On 03/07/2007 08:33 AM, Julianm Macoveanu wrote:

 Hi guys,

 I need some help with basic stuff. I