Morgan,
I just sent you an off-list post about the AAL stuff. It looks like
there are some useful parcellation schemes that we should be able to get
onto PALS_B12 via Colin, if we can overcome some minor obstacles. But
I'm not sure if we'll actually update the colin atlas. Evidently colin
is still being actively used in volumeland. David can think this over.
If you're using AFNI to set the AC-PC and talairach markers, then you
can use AFNI's adwarp command line utility to warp your anatomical from
+orig to +acpc view (rather than +tlrc view); either +acpc or +tlrc
warps would be fine. But if you want your surface coordinates to
reflect "true" talairach, then +tlrc is what you want.
Segmentation is covered here:
http://brainmap.wustl.edu/caret/pdf/Caret_5_12_Tutorial_Segment.pdf
Registration is covered here:
http://brainmap.wustl.edu/caret/pdf/Caret_5_12_Tutorial_Intro.pdf
The latter tutorial still cites the colin atlas as the target (lots of
documentation needs updating). But this page has links to the PALS_B12
target borders:
http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html
It also contains colin ref for landmark borders. In your case, draw
your individual's registration borders using the Core6 landmark guidance
at the web page above. Then, why not run the registration two ways,
using the same individual landmark borders both times, but in the first
pass using colin as the target, and in the second using PALS_B12 as the
target. Then, you can apply the corresponding deformation map to bring
your individual's data to the target of choice and vice versa. Running
the registration takes only five or ten minutes and is fairly painless.
In short, enjoy the best of both worlds.
When you run the to-colin registration, make sure you use the
ref-for-landmarks datasets linked from
http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html
(i.e., that use the core6 landmarks). The tutorial dataset may have
been created before Core6 landmarks were developed.
Donna
On 09/22/2005 10:23 AM, Morgan Hough wrote:
Donna,
Thanks again for the advice.
AAL and the SPM Anatomy toolboxes are both (yes you guessed it) SPM
toolboxes. They both use the Colin brain (or more formally the ICBM
high-resolution single subject template). AAL labels 45 areas in each
hemisphere and the SPM Anatomy toolbox has the Amunts/Zilles cyto data.
If you are going the SPM route then Marsbar adds some more SPM
integration to AAL but it is still all MATLAB.
I would prefer to use Caret to get the same info if I can. I don't know
what might be comparable to AAL in Caret but since Colin is already
registered to PALS you can add the labels from:
http://www.cyceron.fr/freeware/
So in my case single-subject case you would recommend a volumetric
registration and then a segmentation and surface registration to PALS.
Is the volumetric registration just for AC-PC? For a project related
reason I am trying to use AFNI to set manual Talairach markers to get
into "true" Talairach coordinates. Would that be good enough for
pre-segmentation alignment? If that suffices (and I still haven't gotten
AFNI to work right yet:), is the 4.6 segmentation tutorial the next
step?
Thanks again for any advice. I will try and get in touch with Johannes
too.
Cheers,
-Morgan
On Thu, 2005-09-22 at 08:04 -0500, Donna Hanlon wrote:
Hi Morgan,
See comments below.
Also, have you met Johannes Klein, who also works in the FMRIB? He has
extensive experience with Caret registration.
Donna
On 09/22/2005 06:49 AM, Morgan Hough wrote:
Donna,
Thanks for your email. I was just following the instructions at the top
of this page:
http://brainmap.wustl.edu/help/mapper.html
It's on my do-list to update this page (along with several others), but
was there a page that linked to here? If so, I think I'll remove that
link, because this page is so out-of-date (although still helpful for
those that are still using colin and/or older versions of Caret).
which solicits nominations. The email is set to [EMAIL PROTECTED] which
I guess gets forwarded to the list.
Yeah, John got tired of the spam, so we aliased that address to the
list, which allows only member posts.
That said, I am very interested in using caret to visualize results and
look at the correspondence to probabilistic cyto maps, etc. These data
are 99 FMRI sessions across three tasks collected from a single subject.
It is rather complicated but I am only just getting into caret and your
email is very helpful. So if I am doing all my analysis with FSL tools
and I have a high-resolution structural image for this single subject I
should still FLIRT to MNI 152?
There are some good reasons to spatially normalize before segmenting,
but they typically apply to inter-subject analyses.
One reason that applies to single subject analysis is that it eases
drawing of borders by ensuring AC-PC alignment. Just making sure the
subject is well aligned to AC-PC makes it easier to draw borders during
flattening, because the template frontal cut almost always intersects
the medial wall border posterior to the olfactory sulcus. Also, when
drawing the registration borders, you don't need to rotate the surface
to approximate AC-PC alignment (e.g., when figuring out the starting
point for the aSTG landmark).
Since I only have one subject I can take
the time to do a better fit if a better fit is possible. Maybe Colin is
not the best approach (although it was tempting because I would like to
look at the AAL correspondence as well).
What is AAL?
Should I take a surface based
approach for this single subject to get the "best" fit. Thanks again for
your time.
What you're doing is definitely not the mainstream (inter-subject)
registration application, so in some ways I'm tempted to say go ahead
and use Colin. Most of the partitioning schemes available in the
PALS_B12 atlas were actually registered via colin, so they're more
"upstream" in the colin atlas. That said, the colin atlas doesn't have
the Amunt/Zilles cyto areas fMRI mapped, whereas PALS does (see PALS
tutorial -- Caret version, not webcaret at
http://sumsdb.wustl.edu:8081/sums/directory.do?dir_id=6332260&dir_name=PALS_ATLAS_TUTORIAL).
Also, David often fixes 'nits' he comes across in paint, border, and
coord files, and the PALS_B12 datasets get much more of his attention
than the colin atlas does.
BTW, the PALS paper hit NeuroImage early views. I don't have the link
handy but it is there as well.
Cheers,
-Morgan
On Tue, 2005-09-20 at 08:59 -0500, Donna Hanlon wrote:
Hi Morgan,
Many of our best users are FSL users, so we want to make life as easy as
possible for them. While we don't have Colin in FSL (what we're calling
"flirt") grid, we do have the PALS_B12 surfaces that way:
http://brainvis.wustl.edu/help/pals_volume_normalization/
We're recommending users move from Colin to PALS_B12 -- not only for
multi-fiducial mapping (MFM) of fMRI data, but *especially* for
registration purposes
(http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html).
See David's PALS paper for many important details:
http://brainmap.wustl.edu/resources/-PALS_ATLAS_June14_05.pdf
We're shooing people away from Colin and steering them to PALS_B12.
There might be some specific applications for which it makes sense to
use Colin, but I'd like to have a better understanding of them before
adding more Colin grids. Please elaborate a bit more on the requirement.
Space-dependent grids (more accurately in our context, volume
registration method dependent fiducial surfaces) generally have been
used to support fMRI mapping of group results to a visualization atlas
brain (e.g., Colin or PALS_B12). For registration, we never had
grid-dependent target datasets. This is because registration operates
on the sphere. It does matter what fiducial or average fiducial you use
when you visualize/project your registration results. Again -- there is
a flirt version of the PALS_B12 average fiducial in
CARET_HOME/data_files/fmri_mapping_files.
I realize this is probably somewhat confusing, so please let me know
where I need to be more clear.
Donna
On 09/20/2005 07:37 AM, Morgan Hough wrote:
I just wanted to nominate FSL output for grid support. I would be happy
to help supply any information but I believe you are already familiar
with the FSL tools. Please let me know if there is anything we can do to
make supporting FSL easier (such as for instance supplying Colin so that
people can register to that).
Thanks in advance for your time.
Cheers,
-Morgan
_______________________________________________
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
_______________________________________________
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
_______________________________________________
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
_______________________________________________
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
