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