Taosheng,
I don't think there are any tutorials for doing what you want to do. We
had a tutorial for registering Freesurfer data, but it's pretty
outdated. We have scripts that are more helpful for that, and you may
end up adapting those.
It is possible to generate inflated, very inflated, e
Original Message-
> From: caret-users-boun...@brainvis.wustl.edu
> [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Donna Dierker
> Sent: Thursday, October 08, 2009 1:42 PM
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-users] do sphe
> Thank you. But I do not have the surface ready in caret topo/coord
> form to start with, how to start by using mri hi-res images.
>
> thanks again!
>
> Soha
>
> On Thu, Oct 8, 2009 at 2:28 PM, Donna Dierker
> mailto:do...@brainvis.wustl.edu>> wrote:
>
>
2-883-3270
>
>
>
> -Original Message-
> From: caret-users-boun...@brainvis.wustl.edu
> [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Donna Dierker
> Sent: Friday, September 18, 2009 11:20 AM
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-user
On 10/08/2009 11:01 AM, soha saleh wrote:
> Hi Donna and caret users:
>
> I need to map the functional MRI data onto reconstructed surface of
> our subject's MRI data. Can we do this using caret? If yes please give
> me some help with that.
Yes:
If the surface is already in Caret .coord/.topo fo
nce.
On 10/02/2009 09:37 AM, Donna Dierker wrote:
> See inline below.
>
> On 10/01/2009 02:34 PM, Michael Arcaro wrote:
>
>> Hi Donna,
>>
>> Thanks for the heads up. I'm was a bit confused as to the differences
>> between Caret and Surefit datasets.
eed to project
> back into volume space, so the point of origin should not be an issue
> for me.
>
> Mike
>
>
> On Oct 1, 2009, at 2:24 PM, Donna Dierker wrote:
>
>
>> Mike,
>>
>> Just as a heads up, when SUMA was first developed, Caret and SureFit
>
help.
>
> It also appears that SUMA is looking for a .params file. I generated
> one in Caret from File-> save data file (after loading the atlas
> spec). I assume this should be sufficient.
>
> Thanks!
> Mike
>
>
> On Oct 1, 2009, at 9:38 AM, Donna Dierker wrote:
&g
Hi Mike,
1) F6 dataset: Probably only David knows for sure, but
Macaque.F6.BOTH.SURF-VOL.Std-MESH.73730 is dated 3/9/2007, while
Macaque.F6.BOTH.withF99-Data.Std-MESH.73730 is dated 8/16/2007. Since
they have many files in common, my guess is that the latter was based on
the former, but has
it
> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> > or, via email, send a message with subject or body 'help' to
> > caret-users-requ...@brainvis.wustl.edu
> >
> > You can reach the person managing the list at
> > caret-users-ow...@brainv
Matthew,
It has been a long time since I have segmented/flattened a partial
hemisphere, but if my faulty memory serves me, this has little/nothing
to do with using error correction. You could, I think, segment; edit in
Analyze; and feed the Analyze-edited result back into Caret if you
wanted
the 6 landmarks manually, right?
> With te 6 landmarks I draw, I can do the spherical registration. Is
> this a right way to do it?
>
> Thanks.
>
> Jidan
>
>
>
>
> >
> > Message: 2
> > Date: Thu, 17 Sep 2009 08:43:45 -0500
> > Fr
Original Message-
> From: caret-users-boun...@brainvis.wustl.edu
> [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Donna Dierker
> Sent: Friday, September 18, 2009 9:26 AM
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-users] do spherical regis
Center for BrainHealth - University of Texas at Dallas
> Department of Psychiatry - University of Texas Southwestern Medical
> www.utdallas.edu/research/nprlab
> 972-883-3270
>
>
>
> -Original Message-
> From: caret-users-boun...@brainvis.wustl.edu
> [mailto:c
Hi Jidan,
See inline replies below.
Donna
On 09/17/2009 02:06 AM, z丹丹 wrote:
> Hi,
>
> I already have fiducial surfaces generated by Freesurfer, which are
> all in the MNI space. I want to do spherical registration to an atlas
> spherical surface. The steps i need to do are:
>
> 1, generate the
must use it (SPM2 data).. I will
> follow
> your instructions, thanks!
>
> Soha
>
> On Fri, Sep 4, 2009 at 6:46 PM, Donna Dierker
> wrote:
>
>> You didn't specify the format -- .nii or .hdr/.img. Try to write your
>> volume as .nii and see how it maps. I
caret using the same spmT files?
>
> Thank you!
>
> Soha
> On Fri, Sep 4, 2009 at 3:21 PM, Donna Dierker
> wrote:
>
>> I'm not sure how old your Caret version is, but older versions of Caret
>> couldn't read NIfTI files as .hdr/.img; you had to write them as
I'm not sure how old your Caret version is, but older versions of Caret
couldn't read NIfTI files as .hdr/.img; you had to write them as .nii to
get sensible results. I suspect the left is getting mapped to right and
vice versa, because your Caret version isn't reading the NIfTI volume
properl
It doesn't sound like the same thing, but I thought it worth pointing to
this thread:
http://brainvis.wustl.edu/pipermail/caret-users/2009-June/001760.html
On 08/31/2009 04:09 PM, John Harwell wrote:
> Hello,
>
> I used the data set you listed and I was able to project foci on a Mac
> without
e10.R.Right_Hem+orig.nii.gz
the prams file is Human.case10.R.params_file_22.params
thanks
kaushik
On Mon, Aug 10, 2009 at 11:10 AM, Donna Dierker
mailto:do...@brainvis.wustl.edu>> wrote:
Kaushik,
Can you upload your cropped volume and params file again?
http://pulvi
ks Donna, that worked. I am getting another error saying " out of
> memory, caret terminating". This happens while i am trying to segment
> the volume. Kindly let me know what could be a possible solution
>
> thanks
> kaushik
>
> On Thu, Aug 6, 2009
Hi Kaushik,
Thank you for posting to caret-users; I really appreciate it.
Asynchronous communication is a must right now, given very tight
deadlines. But it is always preferrable.
The easiest way for me to diagnose your trouble is for you to upload
your cropped *anatomy* volume here:
http://p
ssage-
> From: caret-users-boun...@brainvis.wustl.edu
> [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Donna
> Dierker
> Sent: 27 July 2009 18:18
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-users] Paint Volume labels for Macaque F99
>
> Hamied,
>
&g
Hamied,
I wouldn't necessarily expect what we call the "paint index" from the
surface/node-based paint file to match the paint index in the LUT_NAMES
list.
But I would expect the LUT_NAMES to accurately map the paint name from
its ordinal position. This post explains how that works:
http://w
figures) as ROIs, and then use these
> ROIs to perform correlaton analysis in fMRI data. I think my
> current problem is how to convert the border data to the volume
> data, i.e. create the volume ROIs base on the fiducial or flat
> border file. Pleas help and sincerely
Hi Dr. Ludwikow,
See inline replies below.
Donna
On 07/21/2009 04:59 AM, eep...@bangor.ac.uk wrote:
> Hi,
>
> I am experiencing some long waiting times while running segmentation
> on a pre-packaged Caret 5.61. Today it amounted to 1 h (when ran
> caret5), the other day to 20 h (when ran car
This will happen every time, if you have only only four columns in
EACHMETRIC.
It can only run a max of 2 to the k iterations, where k is the number of
columns in the metric file -- could be subjects or sessions for a given
subject.
On 07/16/2009 06:04 PM, Akiko Ikkai wrote:
> Hi,
>
> I'm tryi
Talairach
> coordinates at beginning. If not, how can I convert these data to the
> Talairach coordinates?
>
> Best,
> Long
>
> On Thu, Jul 16, 2009 at 2:50 PM, Donna Dierker
> mailto:do...@brainvis.wustl.edu>> wrote:
>
> Hi Long,
>
>
ivate and may contain
> Protected
> Healthcare Information or other information of a sensitive
> nature. If
> you are not the intended recipient, be advised that any
> unauthorized
> use, disclosure, copying or the taking of any action
Hi Krishna,
Sometimes, a screen capture of your main window right before you try
turning voxels off can be enlightening to us. Here are some things that
come to mind:
* The volume is loaded as something other than a segmentation volume --
unlikely, if you're using the tutorial though.
* You hav
reate
> seeds and after calculating, how to create a 'activation map' on a
> flatten cortex and perform the 2D image analysis.
>
> Thanks for your help.
> Long
>
> On Thu, Jul 9, 2009 at 3:05 PM, Donna Dierker
> mailto:do...@brainvis.wustl.edu>> wrote:
&g
Enter "caret5 -help" at the command line. There is an option like
--Cleanlooks or something like that that makes me happy with Caret on my
Linux desktop. Give it a shot.
If it makes you happy, too, consider aliasing "caret" to "caret5
--Cleanlooks" (or whatever the option actually is). I'm not
>> Subject: Sections and MRIs
>> From: "Peter L. Carras"
>> Date: Fri, 26 Jun 2009 18:43:04 -0400
>> To: caret-users@brainvis.wustl.edu
>>
>> To: caret-users@brainvis.wustl.edu
>>
>>
>> Hello,
>>
>> I recently started using CARET (v5.61). I have had some success, but
>> also a few questions that
> Subject: Sections and MRIs
> From: "Peter L. Carras"
> Date: Fri, 26 Jun 2009 18:43:04 -0400
> To: caret-users@brainvis.wustl.edu
>
> To: caret-users@brainvis.wustl.edu
>
>
> Hello,
>
> I recently started using CARET (v5.61). I have had some success, but
> also a few questions that do not seem
rences_file_0caret5_preferences )
>>
>>
>> BeginHeader
>> Caret-Version 5.61
>> date ??? ?? 20 15:41:05 2009 < Chinese time format
>> encoding ASCII
>> EndHeader
>>
>>
>> I restart Caret but Caret keep hanging. Aft
cally
> then crashes. I have tried to reinstall it and it still keeps
> crashing.
> How could I kill the fail process clearly?
> If I can't kill it clearly, I will reinstall the MacOSX to repair
> the Carot and then follow suggestions.
>
> Tha
kill the fail process clearly?
> If I can't kill it clearly, I will reinstall the MacOSX to repair the
> Carot
> and then follow suggestions.
>
> Thanks,
> Midoli :-)
>
>
> On Sat, Jun 13, 2009 at 2:03 AM, Donna Dierker
> wrote:
>
>> If y
If you don't have AFNI installed, you can upload your .hdr here, and I
can try mayo_analyze on my end:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
If you upload the .img file, too, I can try opening it in Caret.
On 06/12/2009 11:43 AM, John Harwell wrote:
> If you tried to load the "img" file,
Hi Michelle,
Okay, you're drawing contours in VOLUME view. This won't work, as far
as I know. Borders only work on surfaces (I think!).
When we want to do what you are trying to do, we use Volume:
Segmentation: Edit Voxels to paint voxels on or off.
But there are a couple of tools I feel com
ally, I tried to change the color of the medial wall
> before I ran deformation and it changed it back to red and BA40? Thank you
>
>
> -Original Message-
> From: caret-users-boun...@brainvis.wustl.edu on behalf of Donna Dierker
> Sent: Thu 6/11/2009 8:41 AM
> To:
See inline below.
On 06/11/2009 09:26 AM, mleis...@artsci.wustl.edu wrote:
> Hi,
>
> I'm just beginning to use Caret, and I'm having some problems with the
> draw border update function. From the information in Caret's help
> function, the draw border update seems to allow you to make alterations
Traci,
I don't understand why the message below bounced. Nor do I really
understand how the paint indices got mixed up.
But you should not need to re-draw the medial wall. Do this:
Surface: Region of interest, selection source Paint, select Brodmann.40
Select node with Mouse, and click in th
I neglected to mention Oliver Lyttelton's OHBM2008 poster, which compared
MNI's CIVET registration with Caret, among other things. It's not the
thorough study that needs doing, but it does illustrate some of the
trade-offs between sulcal alignment and distortions. CIVET is much more
like Freesurf
Hi Donald, & Dav,
As far as I know, neither Fischl et. al. nor VE et. al. has taken this
task on seriously. I vaguely recall someone from MGH registering for
Caret a while back with the research goal of comparing registration
methods. I haven't heard anything since then, and I didn't recognize th
Dear caret-users,
Due to the number of spam messages sent to the list, spoofing addresses
of legitimate members, we have decided to require moderator approval for
all posts. All legitimate posts will be approved; only spam and virus
posts will be rejected.
There have been only three spam posting
Hi Dr. Wang,
Are you by any chance using a BOTH spec file to display your results?
When sorting out problems like this, I find it is helpful to use
hemisphere-specific spec files. For example, the CARET_TUTORIAL_SEPT06
has these three spec files:
PALS_B12.BOTH-HEMS.STANDARD-SCENES.73730.spec
Hi Donald,
You have your pick in /caret_parent_dir/caret/data_files/fmri_mapping_files:
it.wustl.edu 104% grep description *spec | egrep -v '(AFNI|711)'
Human.colin.FLIRT_fMRI-MAPPER.CEREBELLUM.73730.spec:description PC-CC
Cerebellum (73730) converted from Colin Atlas
Human.colin.MRITOTAL_fMRI-M
Hi Sofia,
There is no reason whatsoever you can't map a cubic 1mm volume onto your
surface. In fact, we do this occasionally (e.g., map anatomical volume
onto the surface as if it were a functional volume, to assess the
variation of GM intensity across the cortex).
How much memory do you have
Hi Patrick,
It doesn't look like caret_command currently supports the metric to
RGB_paint feature. I did caret_command -help-full >
/tmp/caret_command.txt and then searched the resulting file for rgb
(case-insensitive). I couldn't find it.
Normally, adding something like this is quick and easy
Hi Sofia,
Let's say you have an activation map (fMRI) in volumetric form for your
subject, for whom you also have a fiducial surface. Provided that the
fMRI has been volume-registered to the same anatomical used to generate
the fiducial surface.
When you map that fMRI volume onto the surface,
ting in a
tighter/crisper mean/sum volume.
On May 1, 2009, at 9:13 AM, Donna Dierker wrote:
>
>> Hi Traci,
>>
>> Glad to hear you solved the index issue. As indicated off-list, these
>> problems are hard to pin down.
>>
>> John Harwell is on vacation for a week,
Hi Traci,
Glad to hear you solved the index issue. As indicated off-list, these
problems are hard to pin down.
John Harwell is on vacation for a week, and my knowledge of the inner
workings of the AC-PC alignment routine is weak.
But I can see how it might need to pad in order to avoid croppin
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
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 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
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
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
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
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
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
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:
>
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
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
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
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,
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
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
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
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
/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
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
>>> 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 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
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 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
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
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 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
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,
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
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
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
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
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
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
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
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
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
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
... 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
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
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 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
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
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
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
.
-----------
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 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).
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
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
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