using FreeSurfer. Can I do registration by these datasets? or if
> not, could you or anyone please upload the datasets which can register
> individual SureFit segmentation with F99 atlas?
>
> Thanks very much,
> TingYu
>
> On Tue, Jun 28, 2016 at 1:25 PM, Donna Dierker
&g
It sure would be nice if sumsdb were working right now, but it's not, and I
have no quick-fix for getting it to work (though we are discussing ideas).
Meanwhile, I'd like to narrow down which F99 individual to F99 registration
dataset you were looking for. If you segmented your monkey's brain u
Hi Ting-Yu,
Hopefully, someone will be able to provide the reference and a link to the
dataset for registering individual monkeys to the F99 atlas. If not, I'll dig
around tomorrow and try to find it.
But I did want to let you know we are aware of the problem with sumsdb. Others
have reporte
Hi Pavel,
Caret cannot segment newborn cortex, but it can flatten hemispheres segmented
using other software (e.g., LIGASE - http://brainvis.wustl.edu/LIGASE).
I thought Fischl et al. were in the process of adding infant segmentation to
Freesurfer. Don't know where that stands, but well worth
On Mar 21, 2016, at 12:44 PM, João Vicente Dornas wrote:
> Dear Rouhi,
>
> thanks for the prompt response.
>
> In fact, I did that already, but the Freesurfer oversample the image to 1 mm.
>
> I had two problems. In one attempt, when I use mri_vol2surf to create my
> labels/annotation files
Hi Julia,
No one has answered your question yet, because it doesn't have a simple answer.
It depends on what you are trying to do, and it might make more sense to work
in workbench, rather caret, depending on what you are doing.
If you have a label.gii, for example, you can view that in either
Hi Simon,
If you can represent your parcellation in Caret paint format, then you can do
Surface: Region of Interest. There is a feature in there that generates areal
borders from parcels. The paint format is defined here:
http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/fil
Hi Dr. Aquino,
No, Connectome Workbench does not offer features like segmentation or
registration (though it does have wb_command features for resampling and
related functions, e.g., -surface-project-unproject). Our lab typically uses
software derived elsewhere for segmentation (e.g., Freesurf
sheep brains.
>
> Thanks again for all the help.
>
> Cheers,
> Rosita
>
> On Tue, Jan 12, 2016 at 3:41 AM, Donna Dierker
> wrote:
> Hi Rosita,
>
> None of the parameters in these commands makes sense for sheep:
>
> > caret_command -volume-creat
the surface *.stl and its converted version to *.pial that I
> > used as the input for Caret.
> >
> > The folder also include a text file containing commands that I used. For
> > some reason I can not run caret commands in my terminal so I use caret
> > command executor.
ed using SURFACE TO SEGMENTATION
> VOLUME), it includes just few voxels in a raw.
>
> Any help would be greatly appreciated.
>
> Thanks,
> Rosita
>
>
> On Thu, Sep 3, 2015 at 12:36 PM, Donna Dierker
> wrote:
> Hi Rosita,
>
> This zip archive has a scrip
This message is for Rosalia, but I have changed the subject line, to keep the
previous thread focused on Julia's monkey surface issues.
There are several Caret tutorials here:
http://brainvis.wustl.edu/wiki/index.php/Caret:Documentation
This one gives you a pretty good overview, but takes a day
Hi Julia,
I confess I don't know these scripts inside and out, but this image is
enlightening:
http://brainvis.wustl.edu/pipermail/caret-users/attachments/20151222/180ba486/attachment-0001.png
It looks like there is a hole in the surface at the occipital pole -- almost
like perhaps Caret cut o
Hi Rosita,
This zip archive has a script named gen_depth.sh:
brainmap.wustl.edu/pub/donna/US/UCDAVIS/cwn.zip
login pub
password download
You'll need to adapt it to your data, but it will give you a head start.
Donna
On Sep 2, 2015, at 7:01 PM, Rosita Shishegar
wrote:
> Hi,
>
>
> I am a
results using the two paths
>>>>>> mentioned above, I think you will solve your problem when you solve
>>>>>> the
>>>>>> misalignment between your cropped volume and the whole brain
>>>>>> anatomical
>>>>>> volu
fset
>>>> you
>>>> need.
>>>>
>>>>> thank you.
>>>>>
>>>>>
>>>>> Hi John,
>>>>>>
>>>>>> Got your upload. While I couldn't open the cropped volume in caret
&g
l paint column as an overlay on top of the functional
> overlay?
>
> Many thanks!!!
> Daniel
>
> On 8/19/15, 6:38 PM, "caret-users-boun...@brainvis.wustl.edu on behalf of
> Donna Dierker" do...@brainvis.wustl.edu> wrote:
>
>> Could you elaborate
Could you elaborate on how you are using caret_command?
The Enable Medial Wall Override affects display, which is not applicable using
caret_command, unless you are using -show-scenes, in which case you would
select the medial wall paint column as an overlay on top of your functional
overlay, i
t;>>> might contain the [XYZ]min values from the cropping, which might be
>>>> used
>>>> to either adjust the functional volume's origin, or more likely apply
>>>> an
>>>> affine transform to the surface, to shift it back into alignme
r.
>> The polarity of the shift (+ or -) depends on whether you're shifting the
>> volume or surface, and I always get confused about it. Usually I try it
>> one way; look at the result like the capture below; and if it looks worse,
>> I try it the other way. ;-
Could you upload your dataset in a zip archive here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
Specifically I need:
* functional volume being mapped
* anatomical volume with which functional volume aligns
* anatomical volume used to generate segmentation -- *cropped*
* fiducial coord file
* t
What software was used to reconstruct the surface?
With freesurfer, there is an offset between the orig.mgz and the surface. And
depending on many factors, you might have to flip/rotate the surface to be in
the same orientation as the volume (or bring the volume to the surface).
See this threa
This almost always is because the functional volume is not stereotactically
registered to the anatomical volume used to generate the fiducial surface. Is
this an atlas surface (e.g., one of the PALS mean midthickness surfaces), or is
it an individual's surface reconstruction? If atlas, this cou
Hi Leonardo,
It is possible that one more skilled than I could get Statistical Paint Report
to do what you want with less trouble. But for me, scripting it via the
command line would be more straightforward. Have a look at two scripts here:
http://brainmap.wustl.edu/pub/donna/WUSTL/BURTON/SCR
Hi Adnan,
I have run into those kinds of errors, and it can be very puzzling/frustrating.
A couple of common triggers:
* If you have a non-english character set installed on your computer/login,
then this can sometimes cause read/write issues. Removing the non-english
character set sometimes
> From: Bill Mills
> Date: Tuesday, June 23, 2015 at 4:17 PM
> To: Software Carpentry Discussion
> Subject: [Discuss] New Paid Fellowships at the Mozilla Science Lab
>
> Hi folks,
>
> We're very excited to announce that applications are now open for three paid
> fellowship positions at the Mo
PM, Frédéric Roux wrote:
> Hi Dona,
>
> thanks for getting back on this.
> I am using NIFTI, so nothing rare from that side.
>
> Just uploaded the file via the link you sent me.
>
> Thanks for looking into this.
>
> --
> FR
>
> - Original Mess
quot;SureFit Caret, and SuMS software users"
> Sent: Saturday, June 20, 2015 11:37:53 PM
> Subject: Re: [caret-users] Missing parts in MyelinMap+Different number of
> nodes!
>
> Yes please use the HCP pipelines for myelin mapping.
>
> Peace,
>
> Matt.
>
> On 6/1
Hi Xara,
Because you are in the enviable position of having high res T1 AND T2, you may
be able to use the Human Connectome Project pipelines on your data, rather than
this (older generation) caret-based myelin mapping script:
http://www.humanconnectome.org/documentation/HCP-pipelines/
This al
create new scale palette?
> 11 июня 2015 г. 18:02 пользователь "Donna Dierker"
> написал:
> Hi Pavel,
>
> Map your volume as a Paint ROI volume, rather than as a metric. Then use
> Attributes: Area Color to assign colors. Save not only the resulting paint
> fil
Hi Pavel,
Map your volume as a Paint ROI volume, rather than as a metric. Then use
Attributes: Area Color to assign colors. Save not only the resulting paint
file, but also the area color file. The paint file has the index to name
mapping, while the area color maps name to color.
If you're
Hi Leonardo,
Given the nature of the data you are mapping, I would expect fragmentation.
This thread might help:
http://brainvis.wustl.edu/pipermail/caret-users/2014-August/006199.html
Hcp-users might yield more feedback on other strategies for accomplishing your
goals.
Cheers,
Donna
On Ma
Hi Bonnie,
With the cutting handles stuff, you are treading into territory I fear, so
can't help you there.
But with the term-12 atlas, I think you can just browse this paper:
Hill, J., Dierker, D., Neil, J., Inder, T., Knutsen, A., Harwell, J., Coalson,
T. and Van Essen, D. (2009) A surface-b
Using either Surface: Region of interest or caret_command
(-surface-region-of-interest-selection and -paint-assign-to-nodes), you can
threshold your metrics at some value and assign a paint/llabel/ROI to them.
Your paint name might be "visual" or "auditory," but it gets mapped to an
integer wh
First, make sure the computer you're using doesn't have a non-English character
set installed, because that often interferes with the Qt file I/O.
Second, make sure the spec file you're selecting has write permission. If
necessary, copy it to a different filename and make sure it is writeable.
Save paint volume as wunil ifh and see this thread:
https://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg03136.html
Sent from my iPhone
> On Jan 18, 2015, at 3:12 AM, Zhijiang Wang wrote:
>
> Hi, all caret experts and users,
>
> I saved the brodmann atlas as a volume file from Caret
Hi Hellen,
Okay, I think you are using MNI's standard mesh, and David performed a
registration between MNI and PALS ~2008, so that bridge exists (i.e., it should
not be too hard to get the Brodmann parcellation onto the MNI mesh).
But it sounds like you want to do a Brodmann Area (BA) lookup in
Scroll down to the Windows XP section:
http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/installation/caret5_installation.html
But that out of memory error still makes me wonder about the character set.
Unless you have a user/pc that has only an english character set that you could
try in
ta field has
> > 4 columns whose meaning I don't understand as well. Could you please
> > clearify this for me and tell me
> > how to get a ROI-number for each vertex?
>
> The atlas label/paint file may have multiple columns for multiple
> parcellations (e.g., LVE00
or each vertex?
The atlas label/paint file may have multiple columns for multiple parcellations
(e.g., LVE00 vs OrbitalFrontal). You might need to extract just one of these
and work with a single parcellation at a time. This is my best guess as to
what is going on there.
>
> Much
You have six bins, like below, but compressed to 0:1? Hmmm. Scratching my
head on that one.
On Dec 11, 2014, at 9:30 AM, "Caspar M. Schwiedrzik"
wrote:
> Hi Donna,
> I followed your advice and compressed the scale into 0:1.
> One more question: While the colors are displayed correctly now
r system.
>
> Catherine
>
>
> On Wednesday, December 3, 2014 9:50 AM, Donna Dierker
> wrote:
>
>
> I was able to open the spec file you uploaded with no problem. There are no
> volume files and not that many surface files, so I doubt memory is an issue.
>
> I d
bit. The spec file is
> Human.PALS_B12.B1-12.DEPTH_ANALYSES_LEFT.73730.spec, which is included with
> the software. I have uploaded the file as Human.PALS.LEFT.zip.
>
> Thanks,
> Catherine
>
>
> On Wednesday, December 3, 2014 8:58 AM, Donna Dierker
> wrote:
>
>
> H
Hi Catherine,
What caret version did you try?
If the spec file is available on a website, can you point me to it?
If not, could you zip up its contents and upload the zip file here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
I'll see what happens when I try to load it.
Donna
On Dec 2, 201
Hi Caspar,
If you converted from Freesurfer, rather than mapping independently in Caret,
then this is puzzling.
I believe mris_convert can now convert directly to GIFTI (.gii) format, and I
suspect this route might be more reliable than converting .w to .metric. Have
you tried this? Probably
I think you should be able to write a palette like that:
http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#paletteFile
The palette file format was originally intended to be compatible with AFNI,
which may have palette editing capabilities of which I am unaware
There is a paint file that comes with many of the PALS-B12 datasets (e.g., Sept
2006 tutorial) that has a medial wall column. Use that as the primary overlay
with your metric or other overlay as the secondary overlay. This grays out the
medial wall.
On Nov 9, 2014, at 10:43 AM, Frédéric Roux
> for each vertex so that I can view it in matlab).
>
> I would appreciate it if you find the time to provide some comments.
>
> Kind regards,
> Rikkert
>
>
>
>
>
>
>
> On Tue, Nov 4, 2014 at 11:09 PM, Donna Dierker
> wrote:
> I doubt y
et-format (if that's possible).
>
> Would this be a good way to go?
>
> Kind regards,
> Rikkert
>
>
>
> On Tue, Nov 4, 2014 at 5:54 PM, Donna Dierker
> wrote:
> Try this one:
>
> http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/PALS_B12/Human_
ms that there is no such file (nor coordinate files for the
> fiducial and inflated surfaces). Are some
> files missing or do I do something wrong?
>
> Thanks and kind regards,
> Rikkert
>
>
>
>
> On Fri, Oct 31, 2014 at 4:27 PM, Donna Dierker
> wrote:
> On Oct 3
-suited for modeling. If you think, though, that this is the best
> option for the creation of a surface-atlas, then I will go for it.
See how far you get with the easy option. If not far enough, then it's
possible the McLaren atlas mesh is in register with F99. I can't recall
clea
a
> paint file. I got the area size of the region using the paint file.
>
> Is there any step wrong?
>
> Thanks!
> Zhiwei
>
>
>
> At 2014-10-30 00:27:14, "Donna Dierker" wrote:
> >Hi wangzhiwei,
> >
> >I'm a little confused by the
On Oct 29, 2014, at 10:56 AM, "HINDRIKS, RIKKERT"
wrote:
>
> Dear all,
>
> I have an averaged T1-image and co-registered volumetric atlas of the macaque
> brain (which has been digitized by a collaborator) and want to derive from it
> a surface-based
> atlas. Subsequently, I would like to us
Hi wangzhiwei,
I'm a little confused by the question. There mention of area size and scales
hints that there might be a confusion between tools used for quantification /
significance testing and those used for display purposes.
Freesurfer has its own tools for significance testing, so you coul
Hi Aditya,
On monkeys, yes. Humans, no. The SureFit algorithm that is in Caret's
segmentation feature was designed for cubic 1mm human data. It worked
reasonably well on higher res monkey data, but some of the subroutines will
likely break on higher res human data (e.g., disconnecting eye, s
If you have individual func.gii files, then it makes sense to view them on your
individual's midthickness surface. If you have group data, you might use an
atlas dataset as your viewing substrate. It doesn't look like there are any
32k versions of Conte69 available for caret5 format:
http://s
a's name is data.nii. So I think it is NIFTI.
>
>
> From: caret-users-boun...@brainvis.wustl.edu
> [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker
> [do...@brainvis.wustl.edu]
> Sent: Sunday, September 28, 2014
_
> From: caret-users-boun...@brainvis.wustl.edu
> [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker
> [do...@brainvis.wustl.edu]
> Sent: Thursday, August 28, 2014 3:47 PM
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-users] proje
Hi Yu,
I juse checked, and you can have only one palette at a time, even though you
can have multiple metric overlays. When you tweak metric settings, it affects
all metric overlays (at least the palette).
There is a way to channel up to three metrics into a RGB map (Attributes:
Metric: Conve
Actually, this is the one I meant to forward...
Begin forwarded message:
> From: "Jennifer Elam"
> Subject: [HCP-Announce] Connectome Workbench v1.0 Released
> Date: September 10, 2014 5:22:28 PM CDT
> To: ,
>
> News from the Human Connectome Project (HCP)
> September 10, 2014
> Connectome Wo
Begin forwarded message:
> From: "Jennifer Elam"
> Subject: [HCP-Users] HCP Pipelines v3.4.0 Released
> Date: September 10, 2014 5:31:47 PM CDT
> To: ,
> Cc: f...@jiscmail.ac.uk, freesur...@nmr.mgh.harvard.edu
>
> News from the Human Connectome Project (HCP)
> September 10, 2014
> HCP Processin
t;
> From: caret-users-boun...@brainvis.wustl.edu
> [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker
> [do...@brainvis.wustl.edu]
> Sent: Wednesday, August 13, 2014 2:27 PM
> To: Caret, SureFit, and SuMS software users
>
Try saving the paint volume as wunil ifh format. Then read the resulting .ifh
file (a text file). The integer : label mappings are there, but there is a
translation of two, if I recall correctly.
You could also convert the surface paint file to text and look just after the
header; that mappin
aret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson
> [tsc...@mst.edu]
> Sent: Tuesday, August 12, 2014 7:16 PM
> To: Caret, SureFit, and SuMS software users; Donna Dierker
> Subject: Re: [caret-users] projecting functional MRI to gii surfaces
>
> -spec-file-cha
(a pair of double quotes) for the argument.
>
> Since you asked something related on the hcp_users list (wb_command volume to
> surface mapping), I will recommend that you try using wb_command for this, as
> caret5 is no longer under active development. The main hurdle in moving to
you
> tell me the method in detail?
>
> thank you
>
> From: caret-users-boun...@brainvis.wustl.edu
> [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker
> [do...@brainvis.wustl.edu]
> Sent: Tuesday, August 05, 2014 10:26 A
the voxel coordinates (3 × 3 × 3 mm
> resolution) containing that point in fMRI?
>
>
> From: caret-users-boun...@brainvis.wustl.edu
> [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker
> [donna.dier...@sbcglobal.net]
&g
Yesterday, I ran into two arcane issues worth passing on, one of which was
covered in an earlier thread:
1. First I tried mapping a paint volume onto an atlas surface, but it turned
out the volume was scalar values -- not discrete integers as I'd expected for a
label/ROI volume. Caret generat
l MRI to 164k fs_LR surface. Every subject have 135 volumes. I want
> get fMRI time course for surface vertices of every subject. How should I do?
>
> From: caret-users-boun...@brainvis.wustl.edu
> [caret-users-boun...@brainvis.wustl.edu] on behalf o
How should I do?
>
> From: caret-users-boun...@brainvis.wustl.edu
> [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker
> [donna.dier...@sbcglobal.net]
> Sent: Friday, August 01, 2014 4:02 PM
> To: Caret, SureFit, and SuMS software users
> Cc: Tan
won't display.
On Aug 1, 2014, at 2:47 PM, "Tang, Yan" wrote:
> I am sure that the file exist and the size of file is 446KB. Is It correct?
>
> From: caret-users-boun...@brainvis.wustl.edu
> [caret-users-boun...@brainvis.wu
Hi Yan,
Could you use a terminal window or file manager to check whether the file
exists, and if so, what its size is.
We have seen cases before where the file was just a header -- no data.
Inexplicably, the presence of a non-english character set on the system used
has caused this sort of tr
Eshita,
We usually run each hemisphere with an alpha of .025, to limit left+right alpha
to 0.05.
If you are interested in only one hemisphere, you can run it at alpha=.05.
(And we run paired left-right diffs using .05.)
The report should state the alpha that was used for your text.
Donna
O
tered the result to 112RM-SL, which is also of the
> format of *.nii.gz.
> Now, I want to register the result to F99 volume. But caret seems to
> have a very different file format, I don't know which fle set as reference in
> registration.
>
>
>
Hi Chris,
See inline replies below.
Donna
On Jul 19, 2014, at 10:18 PM, ?? <1039537...@qq.com> wrote:
> Hi, everyone!
>
> I process my monkey dti data on fsl, and have got 2 sample T test
> result on individual volume space.
You say individual volume space. Does this mean t
Hi Alexander,
I know mris_convert can convert Freesurfer surfaces to GIFTI gii format; I
think it can do the same with surfaces.
The nice thing about GIFTI is that both caret5 and workbench (wb_view) can read
GIFTI files.
Donna
On Jun 19, 2014, at 11:26 AM, Alexander Walther wrote:
> dear
t me know...
>
> Kind regards,
> Rikkert
>
>
> On Wed, Jun 18, 2014 at 8:30 PM, Donna Dierker
> wrote:
> Hi Rickert,
>
> Assuming you used File: Open Data File: type = Volume Anatomy File, you
> should see a normal T1w image.
>
> If you see solid white, then
Hi Rickert,
Assuming you used File: Open Data File: type = Volume Anatomy File, you should
see a normal T1w image.
If you see solid white, then please upload the volume here, so we can try to
replicate the problem:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
Donna
On Jun 18, 2014, at 12:32
Are you sure the coord, topo, and metric files all match (i.e., not only that
they have the same number of vertices, but also that those vertices are in
register with one another across data types)?
On May 31, 2014, at 9:28 AM, Alexander Walther wrote:
> hi caret users,
>
> i've just recentl
Hi Alexandre,
This is something that is easier to do with Caret Workbench (wb_view) than with
caret5, I think, but switching would likely require some file conversion and a
learning curve.
I've never displayed both inflated hemispheres in a single caret session, but
it would not surprise me if
Hi Gabriel,
Just looking ahead, there's a good chance reviewers will complain about using
an individual as an atlas target, if you are registering other individuals to
this template. But I don't want to presume to know what/how/why you are doing
this. I just felt better saying this before you
Hi Gabriel,
More detail on how you "created surfaces from my own template" might help here,
but let me extrapolate and provide information that might be relevant.
I assume you want the Brodmann parcellation in the form of surface-based
paint/label or border form (i.e., the kind of thing shown i
e is in Tal space. Is this a problem?
>
> Audrey-Anne Dubé
> Candidate au PhD R/I neuropsychologie
> Université de Montréal
>
>
> On Wed, May 7, 2014 at 11:30 AM, Donna Dierker
> wrote:
> Another thought occurred to me: If you select a 32k version of the Conte69
> atlas
Hi Wilder,
I'm not surprised. Is there a less folded version of the surface you can use
as a drawing substrate? This one looks inflated, but not enough. If you have
a flat or spherical configuration, or even ellipsoid or very inflated, I think
you will have less of this.
If you're drawing o
rror for number of nodes
Hi,
My volume is in Tal space. Is this a problem?
Audrey-Anne Dubé
Candidate au PhD R/I neuropsychologie
Université de Montréal
On Wed, May 7, 2014 at 11:30 AM, Donna Dierker wrote:
Another thought occurred to me: If you select a 32k version of the Conte69
27;s wb_command, if you want to map
directly to 32k mesh surfaces. But we don't have a 32k version of Conte69 in
caret5.
On May 7, 2014, at 9:58 AM, Donna Dierker wrote:
> Hi Audrey-Anne,
>
> Erin and I tried to do that, but you can't see the menu picks very c
; sharing or a screen cast tool? In this way, we may find a way to solve the
> issue faster.
>
>
>
>
> Audrey-Anne Dubé
> Candidate au PhD R/I neuropsychologie
> Université de Montréal
>
>
> On Tue, May 6, 2014 at 9:50 AM, Donna Dierker
> wrote:
> Audrey,
ic:
> contains a different number of nodes than
> Conte69.L.midthickness.164k_fs_LR.coord.gii
>
> Pressed ok
>
> 18. The brain image is displayed, but without my data on it
>
> Can you see if I did something wrong?
>
> Thanks very much
>
>
> Audrey-Anne D
Hi Audrey,
Hmmm. I wonder if this might be because the spec file you name below is part
of the Caret distribution, and it might be read-only. In fact, it's a good
idea for it to be read-only. The files under data_files are intended to be
used by Caret without risk of users writing their anal
Hi Nicky,
I am a little confused by the "wong cuts" comment. Are these partial or full
hemispheres? Generally, the only cuts in the segmentation process are ones
applied directly by the user during patching. There are also cuts applied
during flattening, but that is a downstream step from se
rface mapping with metric?
>
> I want to show something like p < .05 ~ .0001 for example.
>
> Thanks!
> Daniel
>
> --
> Daniel (Yung-Jui) Yang, Ph.D.
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> Tel: (203) 737-5454
> E-mail: yu
Hi Daniel,
The palette isn't used in the mapping step (caret_command
-volume-map-to-surface or -volume-map-to-surface-pals). Rather, it is used
when visualizing the results of mapping (output metric), either interactively
in caret5 or using a ready-made scene or caret_command -show-scene. Th
dy has a FWHM of 14 mm (maybe
> it's due to the normalization in SPM).
>
> Regards,
>
> Hu
>
>
> -Original Message-
> From: caret-users-boun...@brainvis.wustl.edu
> [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Donna Dierker
> Sent: Mond
FT?
> Now I have the metric file, could you tell me how to smooth it or is there
> any way to convert it back to freesurfer which I know how to do smoothing?
> Many thanks!
>
> Regards,
>
> Hu
>
>
> -Original Message-
> From: caret-users-boun...@br
7;s wrong.
>
> Regards,
>
> Hu
>
>
> -Original Message-
> From: caret-users-boun...@brainvis.wustl.edu
> [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Donna Dierker
> Sent: Friday, March 28, 2014 5:07 PM
> To: Caret, SureFit, and SuMS software users
>
Do you have a non-English character set installed on this computer? We have
had issues with writing metric files when a non-English character set was
installed, but the error I recall was worded slightly different.
On Mar 28, 2014, at 1:22 PM, Cheng, Hu wrote:
> Dear Caret users,
>
> I'm try
Caret could do the task by "Copy Surface Paint Column to Paint Volume", but I
> need to select the volume space. So I hope you could give me some advice on
> the selection.
> Cheers,
>
> Zhuangming Shen
>
>
> > -原始邮件-
> > 发件人: "Don
prompt reply. By the way, which space (AFNI, FLIRT,
> FLIRT-222, FNIRT, FNIRT-222, MRITOTAL, SPM, SPM95, SPM96, SPM2, SPM5, T88,
> 711-2B, 711-2C, 711-2O, 711-2Y) should I choose for
> mni_icbm152_t1_tal_nlin_sym_09a.nii ? Thanks again!
>
>Cheers,
>
> Zhuangming
>
&g
Try going here:
cocomac_testing.spec
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6665233
Click the diskette shaped icon just left of the brain thumbnail.
On Mar 7, 2014, at 5:52 PM, Thomas Yeo wrote:
> I would be most interested as well.
>
> Thanks,
> Thomas
>
> On Sat, Mar 8, 20
; or '/', but got '[0-9]'.
Try "grep Dim0 myfile" and make sure this attribute is set to an integer (e.g.,
73730 -- not 74k_f99).
On Feb 7, 2014, at 10:07 AM, Donna Dierker wrote:
> I checked, and there was some off-list exchange between me and the poster,
>
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