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
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 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 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 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 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
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 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
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
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
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
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
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
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>
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
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
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
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 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_
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 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
... 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,
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
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 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
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
>
> 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
>
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
> 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.
>
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
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
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
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
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
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
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
... 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
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
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
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 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 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
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
... 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
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
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
+ 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
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
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
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.
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
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
Place the text into an image at the specified location.
The origin is at the bottom left corner of the image.
The red, green, and blue color components for the text
range from 0 to 255.
But you have to specify the x and y positions of the t
Hi Antoine,
It almost NEVER makes sense to map onto the inflated surface. It OFTEN
makes sense to display data [that has been mapped onto a fiducial
surface] on an inflated surface.
We actually do have a SPM5 surface, but we haven't yet released it,
because the next major Caret release is p
Hi Bayle,
This command worked just fine for me:
caret_command -volume-map-to-surface test.scale.coord test.topo ""
test.out.metric METRIC_ENCLOSING_VOXEL test.nii
That is, I didn't get the errors you cite below; however, I did get the
patchiness described in your other message (see capture).
.
-----------
John Harwell
[EMAIL PROTECTED]
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave Box 8108
Saint Louis, MO 63110
On Sep 23, 2008, at 8:27 AM, Donna Dierker wrote:
Hi Bayle,
I removed your attac
Hi Alireza,
Sorry for the delayed reply, but you happened to catch us at a workshop
on human consciousness; I normally don't work on Saturday, but I'm
headed to day 2 shortly.
A full reply would take more time than I have, but the short answer is
that I don't think Caret does quite what you
ow replaced the previous pdf document and associated
> dataset
> > with newer versions that correct various minor errors. If you
> started
> > taking a look at the previous version, please switch to the
> newer one,
> > and also let us know
e are nearing completion of a separate tutorial document that describes
> how to
> generate foci files and import them into a 'Foci Library' that will be
> introduced into SumsDB. Stay tuned for an announcement regarding that.
>
> David VE
>
>
> On Oc
Hi Quintino,
Post to caret-users@brainvis.wustl.edu rather than
[EMAIL PROTECTED]; the latter address is just aliased
to me, so if I'm out of the office, no one else will see your message.
Posting to caret-users gets many more brains on your question.
As far as I know, there is no way for Car
Hi Bela,
One thing you can do is view your source (and target, if non-standard)
borders on the source sphere. Then, select D/C: Surface Miscellaneous:
Drawing mode: Hide surface. Spin the sphere around (or use the toolbar
buttons to switch from medial, lateral, etc.), and make sure there are
Hi Manny,
I have no Brainvoyager experience, but I map NIfTI to PALS often. Which
version of Caret are you running? John Harwell fixed some NIfTI issues
a while back, but I don't recall exactly when. If you are using the
most recent version (Version 5.61 - 12 November 2008), then those
chan
... this time to the list, so John knows I'm on it.
Original Message
Subject:Re: [caret-users] Mapping BrainVoyager statistical volumes to
PALS atlas
Date: Tue, 02 Dec 2008 07:32:17 -0600
From: Donna Dierker <[EMAIL PROTECTED]>
To: Manny Vindi
I'm emailing from home, and don't have the macaque dataset right at my
fingertips, but whatever parcellations we do have for the macaque should be
exportable to volumetric form using Caret's Attributes: Paint: Map paint to
volume (or something like that). In the resulting dialog, there are two
Sorry I didn't get to this yesterday; I was busy breaking a colleague's
computer. As I explained off-list, there are several parcellation schemes
for the macaque, and it isn't obvious which is the best choice for you,
since we don't have a "AAL" scheme. There is a Brodmann scheme with this
commen
Hi Manish,
The D/C: Metric Settings is what you use to adjust the scale, palette,
etc. in Caret. Keep in mind that Caret doesn't convert stats to
p-values, so you'll need to convert p to t and adjust the metric
settings in terms of whatever loaded statistic is. I hope my answer is
clear, but
Alex,
Can you upload the foci file (or fociproj) here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
To project them to the PALS atlas (as opposed to your own subject's
surface), Caret does need to know which of the surfaces in the Caret
data_files/fmri_mapping_files directory represents the be
t; Thanks for your help,
> A
>
>
> On 14/01/2009 21:56, "Donna Dierker" wrote:
>
>
>> Alex,
>>
>> Can you upload the foci file (or fociproj) here:
>>
>> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>>
>> To project them to t
Hi Sofia,
When I select Surface: Flatten Full or Partial Hemisphere; set
Flattening type to Full Hemisphere (Ellipsoid) and Morph Sphere; and
click on the "Choose Template Borders" on the Border Template Cuts menu,
I see Human Standard Left and Human Standard Right -- just as before.
Based on
Hi Traci,
You have residual problems with the Freesurfer surfaces? How old are they?
I doubt there is anything comparable to the RadialPositionMap (RPM) file
in the Freesurfer subject's directory. (The radial position map is sort
of a probabilistic version of the segmentation; the RPM gets th
You're quite right -- we'll have to fix the message or fix the link.
Meanwhile, here is a good link:
http://brainmap.wustl.edu/pub/caret/caret_distribution.v5.61.zip
login pub
password download
(I think either the login/password below or the one above will work.)
On 03/09/2009 04:30 AM, qwfy12
If your caret_command doesn't have this option, you'll need a more
current one:
SURFACE TO VOLUME
caret_command -surface-to-volume
[-inner inner-boundary]
[-outer outer-boundary]
[-step intersection-step]
Intersect a surface with a volume and assign the specified
column's data of the metric
Hi YSL,
I'm still partial to the September 2006 tutorial:
http://brainvis.wustl.edu/wiki_linked_files/documentation/Caret_Tutorial_Sep22.pdf
It will take the better part of a day to get through it, but it will
probably be worth the time.
Download the .zip dataset here:
CARET_TUTORIAL_SEPT-06
Ping,
I tried replicating this user's problem just now, and I had trouble seeing
the D/C menu when pressing the D/C button in Webcaret. It appears that a
window is launched, but positioned too far to the right of my screen to be
visible. I'm in the FLTC using one of the kiosks right now, which h
Hi YSL,
The voxel IJK means the voxel indices, which are different from the XYZ
coordinates. If you're unfamiliar with voxel indices (aka volume
index), this page might be helpful:
http://www.grahamwideman.com/gw/brain/fs/coords/fscoords.htm
Donna
On 03/17/2009 09:46 AM, life1...@gmail.com w
Matvey,
This page might be helpful, albeit somewhat outdated (July 2005 vintage):
http://brainmap.wustl.edu/pub/donna/RISHI/PARTIAL_HEM_REG/
login pub
password download
It is more concerned with registration, but it appears you get a flat
map for free. I didn't scrutinize it to see how out of s
Hi Sofia,
With the fiducial loaded in the main window, try Layers: Foci: Project
fiducial foci. If that fails, contact caret-users@brainvis.wustl.edu
(cc'd on this message); I'm on vacation until Monday of next week and have
very intermittent email contact.
Donna
> Hi Donna
> I have a problem w
Hi Alex,
That thread is pretty old, and David has been focusing (it pains me to
gratify his penchant for bad puns) a lot of effort on this subject.
Have you seen these tutorials:
http://sumsdb.wustl.edu/sums/stereotaxictocaretfoci.do
Three things come to mind:
* On the D/C menu, make sure the
YSL is still having posting/subscription issues which we are working to
address.
Meanwhile, I am posting YSL's problem, which I have not encountered.
> I'm not able to open .spec file and the caret command spits out a
> message: MultiByteToWideChar: Cannot convert multibyte text.
> Does anybody
Hi Jinhui,
Both Russ Poldrack (UCLA) and Morgan Hough (Oxford) were trying to do
something like this back in September, 2005. Here are a couple of
relevant threads, and there may be others of that vintage:
http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg00712.html
http://www.mail
>>> cited in my
>>>>> first email, I read a csv spreadsheet containing the foci into Caret
>>>>> that
>>>>> had the following format:
>>>>>
>>>>> tag-version 1
>>>>> tag-number-of-cells 20
>>>&
Hi YSL,
What you are seeing is normal -- until you double-click on one of the
scenes, or press the Show Selected Scene, since the first scene is
already selected.
Did you do that?
Donna
On 04/01/2009 09:38 AM, Yune S. Lee wrote:
> Thanks, John.
> I did as you suggested, but it won't still loa
/02/2009 09:06 AM, Yune S. Lee wrote:
> Hi Donna,
> I did select the scene, but couldn't get it loaded until I uninstalled
> Korean language package.
> James had a theory about what caused this issue and he was right.
> Thanks for your answer, though.
>
> Best,
> YSL
entually spitted out "out of memory" message" That
> was resolved after I removed the Korean language package and
> I could see the inflated lateral view (or others) when I did the
> exactly same step.
> Let me know if I'm not still understanding your questions.
&g
From: Markus Thuerling
Organization: http://freemail.web.de/
To: Donna Dierker
Hello Donna,
thank you very much for the fast answer. I saved the SWI-datas as nii-file. The
datas are displayed isotropic and i don't must change the voxel size. But when
i do this (1x1x1mm^3 is not coo
Hi YSL,
Caret's right menu is context-sensitive (i.e., the options depend on
what menu/mode you are in). The nodal options of surface-land don't
apply to volume-land.
Donna
On 04/07/2009 08:39 AM, Yune S. Lee wrote:
>
> Dear Caret users,
>
> While it is a trivial thing, I noticed that rig
Hi YSL,
I think the user interface was tweaked slightly since the tutorial was
written.
Look for the Surface shape Settings page on the D/C page selection menu.
Donna
On 04/07/2009 09:40 AM, Yune S. Lee wrote:
> Dear Caret users,
>
> I'm following the tutorial and on the 2nd line of page 1
and
> -volume-map-to-vtk-model" has been added. It takes as input a VTK
> model file, a functional volume file, and the name of one of the
> default color palettes. The output is a VTK model file with color
> assignments made using the functional volume.
Donna
On 04/07/2009 11
Hi YSL,
Reading through 1.22 Metric files in the September 2006 tutorial will
give you an idea of how average area is useful when multi-fiducial mapping.
There is a tag-column-threshold pos/neg value for each column in the
metric/surface_shape file format. If you select column threshold, the
Hi YSL,
I wonder if you are mapping an Analyze header, and you did/didn't
specify a LR flip when opening the volume file?
If you can convert your volume to NIfTI first, you're better off.
Donna
On 04/09/2009 01:20 PM, Yune S. Lee wrote:
> Dear Caret users,
> I'm wondering why the activation
c unit,
> voxel, in caret.
> Sorry to bug you by casting dumb questions, but again your help would
> be appreciated.
>
> Thanks,
> YSL
>
>
>
>
> Donna Dierker wrote:
>> Hi YSL,
>>
>> Reading through 1.22 Metric files in the September 2006 tutoria
M.
> So, if it's the way caret is, I'm just aware of the fact, or if there
> is any way to flip the template hemisphere, I would like to know about
> it as well.
> Any help would be appreciated.
>
> Thanks,
> YSL
>
>
>
>
> Donna Dierker wrote:
>
e way of how to view? Enclosed is the screen
> captured file (so, without changing the model, the 2nd view
> (inanimate_conservative_R.hdr) will be shown on the left side.
> Again, thanks for your help!
> -YSL
>
> Donna Dierker wrote:
>> YSL,
>>
>> The best help I can give is to convin
On 04/13/2009 08:23 AM, Yune S. Lee wrote:
> I see. Glad to hear that it has nothing to do with any font failure.
> By the way, I went to the paint selection page to see what was mapped
> for the particular column, but I couldn't find it.
> As is shown in the attached, Average-MED-Wall B1-12 was s
way
> something like AAL map in the MRIcron.
> Your help would be again greatly appreciated.
>
> Thanks,
> YSL
>
>
>
> Donna Dierker wrote:
>> On 04/13/2009 08:23 AM, Yune S. Lee wrote:
>>
>>> I see. Glad to hear that it has nothing to do with any
See page 12, Caret 5 User’s Guide to Analysis Procedures:
http://brainvis.wustl.edu/wiki_linked_files/documentation/Caret_5.5_UserGuide_Analysis.pdf
This shows how to view three metrics concurrently, but there is no need
to select a third if none is needed.
On 04/13/2009 03:26 PM, Yune S. Lee w
Hi caret-users,
I'm passing along answers to questions fielded from multiple sources
recently:
Q: How many caret-users subscribers are there?
A: Currently, there are 495 subscribers to
caret-users@brainvis.wustl.edu spread across the world.
---
Q: How do I change my mailing list preferences
Hi YSL,
I'm not aware of any features like AFNI's "Talairach to" or "Jump to
xyz" in Caret; however, there are many ways to navigate quickly. Here
are some tips:
* If you have a reference anatomical volume -- preferably in cubic 1mm
voxels (e.g., MeanBuckner12_FLIRT+tlrc.HEAD) -- that is in r
On 04/21/2009 04:56 PM, Dav Clark wrote:
> Hi all,
>
> I'm a relatively new Caret user... so I am still learning the basics.
> Currently, with multiple brains, I am able to run the segmentation,
> and things look pretty reasonable (except that much of the skull is
> also identified as white
Hi Jeff,
You were only one subscription away from becoming our 500th caret-user!
David has been doing a lot of work on foci, so he'll probably have
better answers than these, but here are my thoughts:
You could load the SPM99 foci on the SPM99 fiducial surface; project
them; and then "unprojec
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