Not as far as I know, but I haven't tried. If John made that enhancement, it
would be in the change log (see caret page).
- Original Message
From: Alireza Salamy <[EMAIL PROTECTED]>
To: Donna Dierker <[EMAIL PROTECTED]>
Cc: caret-users@brainvis.wustl.edu
Sent: Fri
Hi Bayle,
I removed your attachments and placed them in our upload directory, and
I am forwarding your reply to caret-users that got held up due to
message size constraints. I let the first attachment you sent through,
because it was just a bit above the limit, but this message had three
vol
Hi Bayle,
Your problem replicates on my end -- i.e., I get an empty volume when I
view test.nii in Caret (see test.nii.caret.jpg).
When I view it in AFNI, I do see something that might be mouse cortex
(see test.nii.afni.jpg).
The header does look unusual. Here is AFNI's 3dinfo output:
it.
If you truly have generated depth, as you indicated in an earlier
message, you can use it to effectively select STS (via aseg) AND depth
=<-5.0 (or whatever depth you specify -- play around with it). This
would ensure that gyral nodes are excluded.
You can do the selections in separate comman
I forgot the LUT attachment in the previous message.
It would be nice if Caret could import Freesurfer aseg.nii files
directly, but I suppose that is why the GIfTI developers
(http://www.nitrc.org/frs/?group_id=75) are still hard at work. We
appreciate their efforts.
#
# $Id: ASegStatsLUT.txt
+ Re: [caret-users] question
<http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg00440.html>
Donna Hanlon
o [caret-users] question
<http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg01458.html>
j
Hi Terry,
There might be an easier way of doing this. While borderproj files ARE tied to
a specific mesh (e.g., 35946 vs 73730), border files are not. You can try
opening the source borderproj files on the fiducial surface, and then save them
as border files. Then, open the spec file of your
Hi Joost,
The Fornito paper used a ROI approach, i.e., the cingulate sulcus. It
looks like they took great pains to define the region consistently
across subjects, as is the norm; ROI definition (and consistent
delineation) is often the hard part. Assuming Freesurfer 4.05 is new
enough to h
... this time with attachment
On 08/29/2008 08:31 AM, Donna Dierker wrote:
On 08/27/2008 05:05 PM, MCLAREN, Donald wrote:
Does anyone have instructions for drawing the macaque landmarks?
Donald,
There is no monkey-specific registration tutorial since 2003 (Caret
4.6), and that one was using
On 08/27/2008 05:05 PM, MCLAREN, Donald wrote:
Does anyone have instructions for drawing the macaque landmarks?
Donald,
There is no monkey-specific registration tutorial since 2003 (Caret
4.6), and that one was using now obsolete flat-based registration. But
Figure 8.5, p. 37
(http://brainm
Hi Quihong,
Until John can reply, have a look at this caret-users post from a while
back:
http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg01035.html
Note that the GL libraries are now in
/usr/local/caret/lib_linux_software_opengl (replace /usr/local with the
caret distribution
Hi Traci,
I'm on vacation this week, so make sure you continue to post to
caret-users, since I won't be checking mail Wed-Sun.
Go to the Core 6 landmarks page:
http://brainmap.wustl.edu/help/landmarks_core6/landmarks_core6.html
The very first enty under "Links to Datasets" is a target atlas tha
Hi Andrew,
I'm not aware of a Caret feature that ensures uniform resampling, but
the caret_command -deformation-map-apply and -deformation-map-create
features do support non-uniform resampling. Simplify surface will just
reduce the number of nodes; it doesn't ensure uniform spacing.
Have a
Hi Radhika,
The only way to answer that question (will 3dUniformize work) is to try
it on your data. You should also try the other methods listed in the
earlier thread:
http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg01429.html
Based on previous experience with surface coil an
at 6:38 AM, Donna Dierker
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote:
Hi Amit,
See inline replies below.
Donna
On 08/05/2008 01:20 AM, Amit Etkin wrote:
> Hi all,
>
> I'm trying to map my activation map (spm_T's written ou
... this time with capture attached.
On 08/05/2008 08:38 AM, Donna Dierker wrote:
Hi Amit,
See inline replies below.
Donna
On 08/05/2008 01:20 AM, Amit Etkin wrote:
Hi all,
I'm trying to map my activation map (spm_T's written out as .img and
.hdr pairs) from SPM5 onto a
Hi Amit,
See inline replies below.
Donna
On 08/05/2008 01:20 AM, Amit Etkin wrote:
Hi all,
I'm trying to map my activation map (spm_T's written out as .img and
.hdr pairs) from SPM5 onto a surface in Caret, and getting more
confused the more I do. I've gone through the tutorial, can map
ac
John Harwell did think of something else: Did you go back and fix
something in the segmentation; retessellate; and open the borderproj
drawn on the old mesh on the new mesh flat map? This could explain what
you are seeing.
On 07/30/2008 02:51 PM, Donna Dierker wrote:
Hi Traci,
John
sity of Texas at Dallas
University of Texas Southwestern
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna
Dierker
Sent: Wednesday, July 30, 2008 12:54 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] Landmark Issue
The borderpro
The borderproj looks suspect to me, too, but it is better to view the
from flattening borders on a medial view of the inflated surface. These
are typically appended AFTER you have drawn the other landmarks (CeS,
sylvian, and aSTG) on the flat map and projected them. At that point,
you don't r
Hi Radhika,
I can think of a few former Snyder Lab MSTP students who can recall your
pain all too well.
Here are tools commonly used to correct non-uniformity:
* AFNI's 3dUniformize (http://afni.nimh.nih.gov/afni)
* FSL's FAST (after preprocessing with BET, also part of FSL --
http://www.fmr
University of Texas Southwestern
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna
Dierker
Sent: Friday, July 18, 2008 11:42 AM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] FW: Problems during/after flattening
Hi Traci,
Th
u for your help.
Traci Sandoval
NPR Lab
University of Texas at Dallas
-Original Message-
From: [EMAIL PROTECTED] on behalf of Donna Dierker
Sent: Wed 7/16/2008 1:30 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] FW: Problems during/after flattening
Hi Trac
> volume (FullHead) using the automatic BSE algorithm
implemented in
> BrainSuite2 (http://brainsuite.usc.edu/). Please let me
know if you need
>
> help with setting up the parameters.
>
> Best,
>
> Jochen.
>
Hi Traci,
See inline replies below.
Donna
On 07/16/2008 12:11 PM, Sandoval, Traci I wrote:
After I completed the flattening process and go to save all my files,
I receive an error when I try to save the bordercolor file, it says it
is open for writing and cannot save?
I can think of a fe
>
> I have been successful extracting the brain surface from the
F99UA1
> volume (FullHead) using the automatic BSE algorithm
implemented in
> BrainSuite2 (http://brainsuite.usc.edu/). Please let me know
if you need
>
uld it be
valid to use the F99UA12 dataset in this case?
I look forward to hearing from you.
Many thanks.
Best wishes,
Hamied
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Donna
Dierker
Sent: 15 July 2008 17:01
To: Caret, SureFit, and SuMS so
Hi Hamied,
If you mean generate output similar to FSL's BET, then I'd say, no --
not automatically.
In the case of F99UA12, the AFNI volume
Macaque.F99UA1.BOTH.SEGMENT.clean+orig.HEAD in the September 2006
tutorial
(http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595030),
MACAQUE s
Hi Michael,
I tried reading your VTK file (after bzip2 -d
Human.xx00.R.CerebralHull.vtk.bz2), and Caret seg faulted with:
Generic Warning: In
/usr/local/caret_libraries/source/VTK-5.0.2/IO/vtkDataReader.cxx, line 844
Error reading ascii data!
[1]Segmentation faultcaret5 -styl
Hi Xinian,
I was able to get this to work with your data like so:
Map per part 5, sept tutorial (see previous message); you'll get two
metric files (one left, one right) in a single, shared spec.
In the resulting shared spec, delete all extraneous fiducials coord
files (i.e., all except the
... this time with capture
On 07/08/2008 08:34 AM, Donna Dierker wrote:
Hi Xinian,
Yesterday, I sent you this advice off-list:
First, try part 5 of this tutorial:
http://brainmap.wustl.edu/caret/pdf/Caret_Tutorial_Sep22.pdf
Attached are captures I got using procedures described there
Hi Xinian,
Yesterday, I sent you this advice off-list:
First, try part 5 of this tutorial:
http://brainmap.wustl.edu/caret/pdf/Caret_Tutorial_Sep22.pdf
Attached are captures I got using procedures described there.
If you actually want to see both hemispheres in the same window, then
I recom
ing to a vtk model using the Save
option for the Caret coordinate file. This can also preserve surface
coloration. I don't have a lot of experience with this, but John may
be able to provide additional tips now that he is back from Australia.
David VE
On Jun 26, 2008, at 8:46 AM, Donna
Hi Manish,
There is a quick start tutorial (~1 hour) here:
http://brainmap.wustl.edu/caret/pdf/Caret_5.504_Quick_Start.pdf
Pages 11 and 12 cover viewing functional data. When mapping, select
Space = SPM2.
If you have more time (~1 day), a more thorough walk-through is here:
Caret_Tutorial_
Hi Jochen,
It is possible David has information like this squirreled away
somewhere, but the better source for it is Nikos Logothetis, from whom
we obtained the spectacular F99UA1 anatomical scan.
These papers don't cite a particular case number, but may give some
hints (e.g., got a 4.7T sca
Hi Leeland,
I don't think so, but David will correct me if I'm wrong. (John will
return from Australia next week; he would know best.)
There is a way under D/C: Surface Miscellaneous to turn the drawing mode
to Nodes or Hide Surface, but neither of these will give you what you
want. You co
er suggestions tomorrow
thank you
Sofia
----- Original Message -
From: "Donna Dierker" <[EMAIL PROTECTED]>
To: "Caret, SureFit, and SuMS software users"
Sent: Wednesday, June 11, 2008 3:06 PM
Subject: Re: [caret-users] problem with border file
Hi Sofia,
See inline
e with the border saving/reloading is due to
your not projecting; the cause remains elusive.
thank you
Sofia
- Original Message -
From: "Donna Dierker" <[EMAIL PROTECTED]>
To: "Caret, SureFit, and SuMS software users"
Sent: Tuesday, June 10, 2008 2:55 PM
Sub
Hi Sofia,
See inline replies below.
Donna
On 06/10/2008 06:18 AM, Sofia Crespi wrote:
Hi I have a question.
I've designed some closed border on my flat surface in order to use
them for surface region of interest operation.
More precisely I've daone these operations:
1.Layers>Borders>
Hi Akiko,
You're right: caret_distribution.v5.51.Linux.zip has an older version
of caret_command that doesn't support that feature. Instead, it has
caret_metric, which gives the attached output when called with the
-help-cs flag.
To me, it seems like eons ago when John folded those satell
e the image
as
decsribed above?
Thanks again for your help,
Alex
On 09/05/2008 22:18, "Donna Dierker" <[EMAIL PROTECTED]> wrote:
Hi Alex,
You are missing something: The all important Attributes: Paint:
Generate Colors for paints without colors. I want to say you must
hav
int names.
Clear all or part of paint file.
Convert pain column to paint volume.
Edit paint names.
Am I missing something?
I'm sing version Caret 5.51
Thanks again,
Alex
On 09/05/2008 17:57, "Donna Dierker" <[EMAIL PROTECTED]> wrote:
Hi Alex,
Cool! John has added some
5/09/2008 11:33 AM, Donna Dierker wrote:
Hi Alex,
Would you mind uploading your ROI volume
(http://pulvinar.wustl.edu/cgi-bin/upload.cgi)? It has been quite a
while since I've done this, and I know the gotchas are in this case
more case/data dependent than most (e.g., life will be easier
for selecting this with Paint, as their is with metric. In the summary
before proceeding with the mapping however, it does state that AFM will be
performed.
Am I missing something?
On 09/05/2008 14:47, "Donna Dierker" <[EMAIL PROTECTED]> wrote:
Hi Alex,
What you describe is mo
Hi Alex,
What you describe is more like what we call a ROI paint volume, like the
AAL map shown here:
http://http://www.sph.sc.edu/comd/rorden/template.htmlwww.sph.sc.edu/comd/rorden/template.html
When you map in Caret, you have the option of mapping functional as
metric, or Paint (ROI); you
esults as nicely as if we had a SUIT average cerebellar surface
(and don't hold your breath on that one). Still, I think this is kind
of cool.
On 04/21/2008 09:46 AM, Donna Dierker wrote:
Hi Janine,
Your message was addressed to [EMAIL PROTECTED],
which is aliased to me. But in order for i
Hi Swann,
Try:
Attributes: Metric: Clustering and Smoothing
Clustering tab
The Attributes menu has lots of goodies under it.
If you have lots of metric files that need processing, use the command
line utility:
caret_command -metric-clustering
Donnna
On 04/25/2008 06:44 AM, Swann Pichon wr
Hi Sofia,
I confess this *Assign voxels within closed border feature is news to me.
If you save both the border and border color files, and then open these
files later with the flat surface loaded in the main window, then you
should see the borders. But if any other surface is loaded in the m
Hi Janine,
Your message was addressed to [EMAIL PROTECTED],
which is aliased to me. But in order for it to go to all of the
caret-users mailing list, the address should be
caret-users@brainvis.wustl.edu, which I have cc'd. If you are not a
member of caret-users, then you probably won't see
Hi all,
If you have bookmarked this link, it still works:
http://www.mail-archive.com/caret-users@brainvis.wustl.edu/
But if you got to this page from via link from the caret-users archives
page, then note that the link has moved: The recent server upgrade
caused a relocation of the Search A
Hi caret-users,
You may have noticed problems accessing brainvis and/or
sending/receiving messages within the last day or so. I hope they
haven't been too bad, and I think most of them have been resolved.
If you have trouble and can't get through on the list, contact
[EMAIL PROTECTED] direc
Hi Rishi,
I was out Friday.
While Caret has added volume visualization and other features, SUMA has
added another surface-volume interaction stream for AFNI's users. The
combination of these trends has led to the declining relevance of the
AFNI communication feature.
Donna
On 03/15/2008 0
d running after about 85% loading, while Caret tried to generalize average.
Any suggestions?
Thanks,
Amy
- Original Message -
From: Donna Dierker <[EMAIL PROTECTED]>
Date: Thursday, February 21, 2008 5:11 pm
Subject: Re: [caret-users] mapping functional data from SPM5
To: On-Yee Lo
been fully customized for the macaque. However, i would
not expect the behavior you describe.
Try uploading your dataset to
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
Then let Donna Dierker ([EMAIL PROTECTED]) know the filename.
We may be able to debug from our side.
David VE
On Feb 23,
mapped.
What else can I do? Is it possible that the installation was not set
appropriately? How can I check it?
Thanks,
Amy
----- Original Message -
From: Donna Dierker <[EMAIL PROTECTED]>
Date: Thursday, February 21, 2008 3:36 pm
Subject: Re: [caret-users] mapping functional data
? How're them?
Thanks,
Amy
- Original Message -
From: Donna Dierker <[EMAIL PROTECTED]>
Date: Thursday, February 21, 2008 2:34 pm
Subject: Re: [caret-users] mapping functional data from SPM5
To: On-Yee Lo <[EMAIL PROTECTED]>
Cc: Eugene Tunik <[EMAIL PROTECTED]&
installation of caret).
Any suggestions?
Thanks and best,
Gene
Eugene Tunik, PhD, PT
Dept. of Physical Therapy, NYU
http://homepages.nyu.edu/~et38/
- Original Message -
From: Donna Dierker <[EMAIL PROTECTED]>
Date: Wednesday, April 11, 2007 9:28 am
Subject: Re: [caret-users] m
so matches with that of the original
values (0.993 x 0.927 x 1.007 cubic mm)
I will proceed with segmentation now.
Thank you
regards
On 1/30/08, *Donna Dierker* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Hi Niranjan,
I can't replicate the problem withou
Hi Niranjan,
I can't replicate the problem without the .img file, too, but I did look
at just the .hdr, and there were some non-standard things about it
(e.g., pixdim[0]=-1.0). I wondered whether this might be a NIFTI volume
written as .hdr/.img, which Caret doesn't yet support? If so, try
Hi Jay,
How's it goin', eh?
Some reasons come to mind (e.g., average surface doesn't intersect the
volume well), but I'd prefer to have a look myself first. Could you
upload the SPM5 volume here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
Alternatively, you could send a few captures show
Just out of curiosity, how does one do this on Windows? I know how to
do it on Linux (tcsh: setenv
CARET_DEBUG yes; bash: export CARET_DEBUG=yes), but not on Windows. Is this a
registry thing?
On 01/23/2008 10:54 AM, Roland Marcus Rutschmann wrote:
On Wednesday 23 January 2008 17:44, Sofia
The problem is that you're just getting too good at flattening.
On 01/17/2008 03:20 PM, Erin Reid wrote:
Hi Akiko,
You are actually not running into a problem at all. The
flat_cycle5_overlap_smooth is not always created if the surface
doesn't need that extra little attention at the end. If C
Good point -- the PALS_B12 tutorial was intended as a full day tutorial.
The one John cites below is much quicker, but obviously less comprehensive.
John Harwell once said, "You can't have a tutorial called 'The Basics'
that's over 80 pages." Well, I agree. Although the title is
misleading,
Hi Sofia,
It depends on how you want to use Caret, but I still point most users to
the Sept 2006 PALS_B12 tutorial:
CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu/sums/directory.do?id=6585200
Both the tutorial document (PDF) is there, as well as the dataset.
Click on the diskette shaped ico
Hi Hamied,
Sure: Attributes: Paint: Convert paint column to paint volume. Select
the LVE00 column. For Volume Selection, set Parameters using a volume
file and select Macaque.F99UA1.LR.03-11+orig.HEAD.
You'll need to save the resulting Volume paint file, and as I recall,
not all file formats
omical, but not onto the
surface. I think there may be some alignment issues between the original
anatomical and the processed one used for the segmentation/surface. Can you
recommend something to fix this?
Thanks so much,
Sarah
On 12/6/07 10:32 AM, "Donna Dierker" <[EMAIL PROTEC
Hi Jay,
I see it's 8 degrees Fahrenheit in Minneapolis. B.
I don't think Caret does this. Several people have asked for it (e.g.,
Ted DeYoe), and David talked to someone about it recently. But for
whatever reason, it hasn't popped to the top of the priority stack yet
-- at least not to
Hi Sarah,
This is not something we do every day -- map group results to an
individual's surface. Maybe some context might clarify.
But let me illustrate an example where something like this might make
sense. Suppose I have functional group differences, and I want to
investigate whether ana
(CST)
From: [EMAIL PROTECTED]
To: David Van Essen <[EMAIL PROTECTED]>
CC: Roland Marcus Rutschmann
<[EMAIL PROTECTED]>, John Harwell
<[EMAIL PROTECTED]>, Donna Dierker <[EMAIL PROTECTED]>,
David Van Essen <[EMAIL PROTECTED]>
Just one inline reply nea
On 11/26/2007 12:52 PM, Roland Marcus Rutschmann wrote:
On Monday 26 November 2007 18:41, John Harwell wrote:
Roland,
Dear David, Donna, John (in alphabetical order),
thanks for all your informative answers.
Just one more question about this (which is exactly what I was looking for)
Hi Roland,
Wow -- you're right: That flat surface *is* funny looking. My initial
impression is that it's not applying a cut where the padding meets the
real surface, the way it used to. Could you upload your dataset here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
It's been ages since I
Hi Roland,
See inline replies below for a couple of answers. John will be in later
today and probably will know the remaining answers.
Donna
On 11/22/2007 05:31 AM, Roland Marcus Rutschmann wrote:
Hi again,
while working with the new caret version 5.5 I encountered some new (at least
to m
Hi Hamied,
David will know for sure, but I don't see it in any of the paint file
column-names in the September 2006 tutorial. The closest sounding one
was Preuss & Goldman-Rakic 91 Fig 4, the comment for which says:
Preuss, T.M., and P.S. Goldman-Rakic (1991a) Myelo- and cytoarchitecture
of
Hi Joanna,
See inline replies below.
Donna
On 11/08/2007 11:49 AM, Joanna Hutchison wrote:
Hello,
I am a new Caret user, and I am a bit confused by a couple of things that I am hoping can be easily clarified.
First, we use Linux as our primary computer operating system. In the Linux environ
Hi Swann,
With the regular Volume: SureFit Operations (Segmentation), I'm pretty
sure you still need to crop to a left or right hemisphere. So before
launching segmentation, you'd still need to Volume: Resize underlay
volume to crop it. (I say pretty sure, because John Harwell is always
mak
Hi all,
Justin Baker and Jason Vytlacil have made their cell projection tutorial
available in sumsdb. It documents how to align your recording chamber
with monkey surface reconstructions, so you can project cells onto the
surface. The PDF document and zip archive of the tutorial dataset are
Hi Michelle,
I'm forwarding your message to the caret-users list. Your message
appeared to our server as From: [EMAIL PROTECTED] (note the plus sign) --
not [EMAIL PROTECTED], which is the address under which you are subscribed.
Donna
Original Message
Subject:rejec
Jay,
Although I was all set to shame you into learning some scripting, John
recalled a feature that gets you around it for now. The Animate button
on the D/C: Metric: Settings menu cycles through whatever metric columns
are currently loaded. (You can load multiple volumes from disk when
map
Hi Mike,
I don't see it in sumsdb, either, but there is a zip file named like
that here:
http://brainvis.wustl.edu/pub/john/contours/
login pub
password download
John will know whether it's the latest/greatest.
Donna
On 10/24/2007 10:14 AM, Michael Semcheski wrote:
Hello,
I'm working thro
Hi Alex,
Use Attributes: Area Colors to control the color mapping of paint
files. You can't use palette files for paint files, because paint is
ROI/discrete/parcellation, while metric is scalar/continuous/gradated.
Depending on the metric/scalar data, sometimes you can
sum/subtract/multiply
roperly for
comparisons, but caution/thought is needed.
Donna
On 08/30/2007 01:01 PM, Chuan-Chih Yang wrote:
(My replies are also inline :)
Am 30.08.2007 18:43 Uhr schrieb "Donna Dierker" unter
<[EMAIL PROTECTED]>:
Hi Jackie,
See inline replies below.
Donna
On 08/30
umbers.
I'm probably misinterpreting your intent, so please clarify your goal.
Cheers,
jackie
Am 29.08.2007 15:12 Uhr schrieb "Donna Dierker" unter
<[EMAIL PROTECTED]>:
Hi Jackie,
See inline replies below.
Donna
On 08/29/2007 07:16 AM, Chuan-Chih Yang wrote:
Hi Jackie,
See inline replies below.
Donna
On 08/29/2007 07:16 AM, Chuan-Chih Yang wrote:
Dear list,
I got a question about the selection of target space (mapping volumes onto
surface). My attemp is to map the functional zstat.nii of FSL onto N27
template by using caret. I found different tar
s.) In a pinch, you can
even x-flip the atlas target coord files, for the purpose of mapping,
but then display the resulting metric on properly oriented coord files.
Donna
On 08/22/2007 12:56 AM, Roland Marcus Rutschmann wrote:
On Tuesday 21 August 2007 20:32, Donna Dierker wrote:
Hi Ro
Hi Roland,
Select SPM2 from the Space drop-down menu, and then select either or
both of the PALS_B12 left and right options for the Atlas menu (i.e.,
see spm2.jpg).
If this is a .hdr (not NIfTI) volume, then you might need to load the
volume first to x-flip it to left-on-left (see right_on_l
Hi caret-users,
FYI: Our server brainvis had a disk failure this morning that may result
in some things falling through the cracks (mail messages, uploads,
registrations). We think the impact was quite limited, but in case
someone posted around the time of the outage, it's possible it got
ac
Donna
On 08/13/2007 10:18 AM, Donna Dierker wrote:
Hi Cedric,
Did you feed Caret a .hdr/.img pair or a .nii NIfTI volume? I think
you'll have better luck with the latter.
Donna
On 08/10/2007 07:42 AM, Cédric LAMIREL wrote:
Hi,
I’m a new user of caret.
I’m trying to visualise retinoto
Hi Cedric,
Did you feed Caret a .hdr/.img pair or a .nii NIfTI volume? I think
you'll have better luck with the latter.
Donna
On 08/10/2007 07:42 AM, Cédric LAMIREL wrote:
Hi,
I’m a new user of caret.
I’m trying to visualise retinotopic map analysed by SPM5 with Caret.
No problems to seg
Hi Rishi,
When you actually ran the registration, did it complain about crossovers?
It's not hard to get weird results when viewing registration results,
because your deformed spec file has files from both source and target.
For example, deformed flat maps might look funny if not viewed with
grid computing system.
Anthony
Donna Dierker wrote:
Hi Kevin,
Not directly, as far as I know. The closest two such features are these:
* When you multi-fiducial map a fMRI volume onto the PALS_B12 atlas,
you can specify a threshold. Then it maps the volume to each of the
12 PALS_B12
Hi Kevin,
Not directly, as far as I know. The closest two such features are these:
* When you multi-fiducial map a fMRI volume onto the PALS_B12 atlas, you
can specify a threshold. Then it maps the volume to each of the 12
PALS_B12 hemispheres, and calculates the suprathreshold area of each
h
Hi Rishi,
See inline replies below.
Donna
On 08/01/2007 10:23 AM, Rishi Kalwani wrote:
Hi,
I have a registered surface and am trying to map Volume Data to the
surface but the data doesn't show up on the surface.
I have been trying to do this using Volume data saved in Analyze
format (.hdr
Hi Joseph,
See inline replies below.
Donna
On 07/31/2007 06:18 PM, Vu, An wrote:
Hi All,
I was wondering what software people have used in their labs for mapping fMRI
data onto surfaces and getting the alignment done. If Caret can do it, I'm
still unclear on how to turn .img/.hdr or .mat fi
Hi Antonino,
Also, I forgot about this recent, possibly relevant post from David:
http://brainvis.wustl.edu/pipermail/caret-users/2007-July/001250.html
Donna
On 07/30/2007 08:18 AM, Donna Dierker wrote:
Hi Antonino,
Each tutorial has its own dataset, whose scenes correspond to the
tutorial
Hi Antonino,
Each tutorial has its own dataset, whose scenes correspond to the
tutorial narrative. For example, the June 2006 tutorial's dataset is here:
CARET_TUTORIAL_WashU_JUNE06
http://sumsdb.wustl.edu/sums/directory.do?id=6499756
Normally, this link is included in the tutorial document,
Hi Lindsay,
Ferret data -- should have recognized it. You're actually not the first
to use Caret to flatten ferret hemispheres. I'm copying the first
person I know to use it on ferrets. Andy may have some pointers on
ferret cuts.
Donna
On 07/20/2007 01:48 PM, Lindsey Leigland wrote:
Hi.
Hi Lindsey,
I've seen the back side of the compressed medial wall get painted red
when a crossover check is run on that view. So I don't get worked up
about that.
But what I see in window 2 looks strange. This is human data? Partial
or full hemisphere? It just doesn't look like a normal,
Hi Joseph,
I'm not sure, but the problem is with the topo file. If you made any
cuts during the initial flat review stage, did you save your CUT topo
file? Normally, it's not necessary to save the topo file, because Caret
saves it automatically when you run Flatten Full Hemisphere and Morph
Hi Julia,
On your initial flat map, none of the red patches along the edges would
worry me, but we would check the ones I've circled in the attached
capture. By check, I mean click on the red patch in the main window,
but use an inflated view in Window 2 to locate the crossover region in
the
Hi Pedro,
I'm not familiar with "off" format.
You'll need to convert your surface into one of the following file
formats that caret_file_convert (or Caret's File: Import) can read:
BYU input surface is a BYU surface file
This type is followed by the name of the BYU s
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