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
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
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
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.,
> try to see what else may work for my sheep brains.
>
> Thanks again for all the help.
>
> Cheers,
> Rosita
>
> On Tue, Jan 12, 2016 at 3:41 AM, Donna Dierker <do...@brainvis.wustl.edu>
> wrote:
> Hi Rosita,
>
> None of the parameters in these commands ma
minal so I use caret
> > command executor. So, I wrote the name of the used command and their
> > inputs
> > as well as the complete command.
> >
> > Thanks again!
> >
> > Cheers,
> > Rosita
> >
> >
> > On Wed, Jan 6, 2016
the volume (output_volume.nii file created 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 <donna.dier...@sbcglobal.net
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
!!!
Daniel
On 8/19/15, 6:38 PM, caret-users-boun...@brainvis.wustl.edu on behalf of
Donna Dierker caret-users-boun...@brainvis.wustl.edu on behalf of
do...@brainvis.wustl.edu wrote:
Could you elaborate on how you are using caret_command?
The Enable Medial Wall Override affects display
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. ;-) One of the ways usually does the trick.
Donna
On Aug 12, 2015, at 9:14 AM, Donna Dierker do
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
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:
From: Bill Mills b...@mozillafoundation.org
Date: Tuesday, June 23, 2015 at 4:17 PM
To: Software Carpentry Discussion disc...@lists.software-carpentry.org
Subject: [Discuss] New Paid Fellowships at the Mozilla Science Lab
Hi folks,
We're very excited to announce that applications are
PM, Frédéric Roux f.r...@bcbl.eu 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 Message -
From: Donna Dierker do
: 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 6/19/15, 4:17 AM, Donna Dierker do...@brainvis.wustl.edu wrote:
Hi Xara,
Because you
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
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
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 when
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.
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
it in Matlab
with gifti.m (from the GIFTI toolbox). I then have all 19 columns at once!
Now you have to ponder which are useful to you.
Kind regards,
Rikkert
P.S. I noticed that in the Paxinos atlas, V5 is merged with the medial wall.
On Thu, Jan 8, 2015 at 3:51 PM, Donna Dierker do
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
cschwie...@mail.rockefeller.edu wrote:
Hi Donna,
I followed your advice and compressed the scale into 0:1.
One more question: While the colors
On Wednesday, December 3, 2014 9:50 AM, Donna Dierker
do...@brainvis.wustl.edu 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 don't know why it is hanging on win7
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?
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
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
.
Kind regards,
Rikkert
On Tue, Nov 4, 2014 at 11:09 PM, Donna Dierker do...@brainvis.wustl.edu
wrote:
I doubt you'll be able to convert the deformation map to Caret, but it won't
be necessary, if Spherical Demons can resample what you need onto the source
or target mesh, after
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 do...@brainvis.wustl.edu
wrote:
On Oct 30, 2014, at 11:29 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu
wrote
way to go?
Kind regards,
Rikkert
On Tue, Nov 4, 2014 at 5:54 PM, Donna Dierker do...@brainvis.wustl.edu
wrote:
Try this one:
http://brainmap.wustl.edu/pub/donna/ATLASES/HUMAN/PALS_B12/Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.SPHERE.borderproj
login pub
password download
On Oct 29, 2014, at 10:56 AM, HINDRIKS, RIKKERT rikkert.hindr...@upf.edu
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
?
Thanks!
Zhiwei
At 2014-10-30 00:27:14, Donna Dierker do...@brainvis.wustl.edu wrote:
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
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
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,
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:
...@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] projecting functional MRI to gii surfaces
Hi Yan,
There are lots of ways to split up the brain
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:
.
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
Subject: Re: [caret-users] projecting functional MRI to gii surfaces
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
of Donna Dierker
[do...@brainvis.wustl.edu]
Sent: Tuesday, August 05, 2014 9:14 AM
To: Caret, SureFit, and SuMS software users
Cc: Tang, Yiyuan
Subject: Re: [caret-users] projecting functional MRI to gii surfaces
I'm not clear on what you mean by I want get fMRI time course for surface
vertices
...@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-change-resolution will not get you to the fs_LR 32k atlas from
fs_LR 164k (but it may get you deceptively
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 AM
To: Caret, SureFit, and SuMS software users
Cc: Tang, Yiyuan
Subject: Re
...@brainvis.wustl.edu
[caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker
[donna.dier...@sbcglobal.net]
Sent: Friday, August 01, 2014 5:34 PM
To: Caret, SureFit, and SuMS software users
Cc: Tang, Yiyuan
Subject: Re: [caret-users] projecting functional MRI to gii surfaces
Push
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
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
of Donna Dierker
[donna.dier...@sbcglobal.net]
Sent: Friday, August 01, 2014 10:10 AM
To: Caret, SureFit, and SuMS software users
Cc: Tang, Yiyuan
Subject: Re: [caret-users] projecting functional MRI to gii surfaces
Hi Yan,
Could you use a terminal window or file manager to check whether
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.
ChrisTang
tangzhenc...@fingerpass.net.cn
Donna Dierker
?? 2014-07-21 23:34
...
Kind regards,
Rikkert
On Wed, Jun 18, 2014 at 8:30 PM, Donna Dierker do...@brainvis.wustl.edu
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 please upload the volume here
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
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
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 awaltherm...@gmail.com wrote:
hi caret users,
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 in
Université de Montréal
On Wed, May 7, 2014 at 11:30 AM, Donna Dierker do...@brainvis.wustl.edu
wrote:
Another thought occurred to me: If you select a 32k version of the Conte69
atlas as your spec file, then you'll get an error when you try to open the
164k vertex metric file. I'm sure
? 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 do...@brainvis.wustl.edu
wrote:
Audrey,
I will look at this more closely later
, 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 do...@brainvis.wustl.edu wrote:
Hi Audrey-Anne,
Erin and I tried to do that, but you can't see the menu picks very clearly in
the video
] mapping ALE on surface: error 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 do...@brainvis.wustl.edu wrote:
Another thought occurred
my data on it
Can you see if I did something wrong?
Thanks very much
Audrey-Anne Dubé
Candidate au PhD R/I neuropsychologie
Université de Montréal
On Wed, Apr 30, 2014 at 3:22 PM, Donna Dierker do...@brainvis.wustl.edu
wrote:
Hi Audrey,
Hmmm. I wonder if this might be because
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
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.
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: yung-jui.y...@yale.edu
On 4/8/14 2:19 PM, Donna Dierker do
Message-
From: caret-users-boun...@brainvis.wustl.edu
[mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Donna Dierker
Sent: Monday, March 31, 2014 11:07 AM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] mapping fMRI data to surface
Hi Hu,
No, there's
(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: Monday, March 31, 2014 12:18 PM
To: Caret, SureFit, and SuMS software
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
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: Donna Dierker do...@brainvis.wustl.edu
发送时间: 2014年3月20日 星期四
收件人: Caret, SureFit
. 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
-原始邮件-
发件人: Donna Dierker do
no.503-614-3755
Mob No.-503-799-7204
On Thu, Feb 13, 2014 at 9:02 AM, Donna Dierker do...@brainvis.wustl.edu
wrote:
Hi Ahmad,
Even if your anatomical volume is in LPI orientation, I don't think your
surface is. Does the segmentation volume used to generate that surface align
properly
Research Center (ONPRC)
Oregon Health and Science University (OSHU),Portland
Oregon- 97006
Ph no.503-614-3755
Mob No.-503-799-7204
On Thu, Jan 16, 2014 at 5:42 PM, Donna Dierker donna.dier...@sbcglobal.net
wrote:
When I see something like that, I wonder if your fiducial surface
hemisphere).
Thank you,
Eshita
On Fri, Feb 7, 2014 at 1:13 PM, Donna Dierker do...@brainvis.wustl.edu
wrote:
Maybe I am the one who is mistaken, but I thought this is how these columns
behaved. I would be more than happy to look at your *significan*metric if
you want to upload
I checked, and there was some off-list exchange between me and the poster, but
it didn't address this error, per se.
The solution for this user was to use mri_convert to reorient rawavg.mgz, which
was in sphinx orientation, the translate per
threshold to be
0.05. Is there anything else in my settings that may be contributing to this
error?
I have 35 controls and 60 treatment subjects. I am looking into running the
two-sample t-test instead of anova.
Thanks for your help!
Eshita
On Wed, Feb 5, 2014 at 3:54 PM, Donna Dierker
AM, Donna Dierker do...@brainvis.wustl.edu
wrote:
Yes, pretty much: I usually have a study directory into which I copy the
Conte69 files. Then I rename the Conte69 spec to something more
study-specific. I usually use the Conte69 inflated and very inflated for
t-map visualization, along
From: caret-users-boun...@brainvis.wustl.edu
[caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker
[do...@brainvis.wustl.edu]
Sent: Thursday, January 30, 2014 11:22 AM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] display myelin mapping results
repeat the procedures on your data?
Hu
From: caret-users-boun...@brainvis.wustl.edu
[caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker
[do...@brainvis.wustl.edu]
Sent: Wednesday, February 05, 2014 9:42 AM
To: Caret, SureFit
groups and want to see where one group is deeper than the
other, you can run a t-test instead of an anova.
Thanks for your help,
Eshita
On Wed, Feb 5, 2014 at 5:58 AM, Donna Dierker donna.dier...@sbcglobal.net
wrote:
Use the D/C: Metric Settings menu to adjust the threshold to .90
of information right below the header, as you
mentioned. But for the TFCE report, I don't see anything similar. Maybe I am
interpreting it incorrectly?
Thank you,
Eshita
On Fri, Jan 31, 2014 at 1:15 PM, Donna Dierker donna.dier...@sbcglobal.net
wrote:
On Jan 31, 2014, at 2:17 PM
I assume you mean this tutorial:
FS-to-F99_Tutorial_Sept10.doc
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8285962
I confess I'm not as familiar with the details of that one, but my hunch is
that the volume is being used here not to drive registration directly, in the
way it would a
On Thu, Jan 30, 2014 at 5:17 PM, Donna Dierker donna.dier...@sbcglobal.net
wrote:
Wow, does this mean you got past the grind-to-a-halt JRE problem? Excellent!
Here is a script I used to compute mean midthickness surfaces for two groups:
http://brainmap.wustl.edu/pub/donna/US/UCLA
copy their spec file and replace
all the files?
Thank you very much!
Regards,
Hu
-Original Message-
From: caret-users-boun...@brainvis.wustl.edu
[mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Donna
Dierker
Sent: Monday, January 20, 2014 6:18 PM
To: Caret
Wow, does this mean you got past the grind-to-a-halt JRE problem? Excellent!
Here is a script I used to compute mean midthickness surfaces for two groups:
http://brainmap.wustl.edu/pub/donna/US/UCLA/ESHITA/gen_mean_fiducials.pared.sh
login pub
password download
But the main command is this
Can you upload your cdv file here (just one of them):
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
And tell us which atlas/tutorial you were using for mapping the foci (e.g.,
PALS or Conte69)?
On Jan 28, 2014, at 3:43 PM, Lauri lort...@yahoo.com wrote:
Dear caret-users,
I am trying to
-users-boun...@brainvis.wustl.edu] On Behalf Of Donna Dierker
Sent: Monday, January 20, 2014 6:18 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] only got one hemisphere from surefit
SureFit only segments one hemisphere at a time. You need to crop to a left
or right
can send you.
On Jan 22, 2014, at 4:27 PM, Eshita Shah eshs...@ucla.edu wrote:
Yes, it works fine at 1000 iterations. I am trying to run 5000. It seems to
get really slow after 1000, but continues on to about 2600 until it crashes.
On Wed, Jan 22, 2014 at 2:13 PM, Donna Dierker do
just downloaded
the JRE you provided, and it is actually the same one that I am using.
Do you think there is another source of this problem?
Thank you,
Eshita
On Wed, Jan 15, 2014 at 7:23 PM, Donna Dierker donna.dier...@sbcglobal.net
wrote:
At the end of the TFCE processing
SureFit only segments one hemisphere at a time. You need to crop to a left or
right hemisphere and run them separately.
On Jan 20, 2014, at 3:36 PM, Cheng, Hu huch...@indiana.edu wrote:
Dear Caret User,
I’m running Caret on a 64-bit Windows. I tried to segment an individual’s T1w
. The new caret5 GUI
works just fine.
Thank you,
--ts
On 11/27/2013 05:18 PM, Donna Dierker wrote:
Good question. You could use different versions for the two steps, but
you'd have to report that in your methods, which could get messy. Running
pre border.sh with the older caret_command
If you have opted to run the registration both ways (individual to atlas and
atlas to individual), you should be able to get the atlas goodies on the native
mesh. If they were not in the spec file when you ran the registration, then
you can apply the deformation map in the native directory to
I have a suspicion: Somehow, you could have gotten a
link/shortcut/caret5-binary-itself on your desktop or some other location that
is displaced from the rest of the caret distribution. (This happened to me
recently, which is why it comes to mind.) In order for caret to see the atlas
spec
and it does finish, although with 144 cycles. Are you saying we
should switch back to the old caret for the time being? I mean, the
check_reg result seems fine, but maybe there's still something wrong with
it?
Thank you!
--ts
On 11/27/2013 11:27 AM, Donna Dierker wrote:
Hi Taosheng
different between
the two groups after statistical analysis.
Thank you,
Eshita
On Thu, Nov 21, 2013 at 4:33 PM, Donna Dierker donna.dier...@sbcglobal.net
wrote:
I would use the Conte69 for TFCE/cluster area computation purposes. Think of
it as a neutral, unbiased atlas surface
the open topo file, but to input into ANOVA should
I be creating an average topo file of all my subjects?
Please let me know. Thank you for your patience and help.
Eshita
On Fri, Nov 15, 2013 at 3:50 PM, Donna Dierker donna.dier...@sbcglobal.net
wrote:
Scroll down eshita
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I doubt it's what you want, but it's the closest I could find:
SYNOPSIS for importing contour files
-file-convert -ic CONTOUR_TYPE input-file-name
caret-contour-file-name [caret-contour-cell-file-name]
DESCRIPTION for Importing Contour
Hi Eshita,
I always use the open topology for this purpose (i.e., excludes only medial
wall vertices). The files here will be helpful:
http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2013_11/TFCE_164k/
login pub
password download
You can get them all in this zip file:
This could happen easily if you are using Caret5 and the same
visualization specification for both hemispheres. If you have both
metric files loaded, but the same metric overlay is set to apply to All
surfaces (see top of metric selection page selection on D/C menu).
Are you mapping to
One quote from Poldrack et al. before I hop off the soapbox:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2287206/
Finally, while thresholds must account for the multiplicity of tests, we do
encourage authors to make available unthresholded statistic and effect size
images in order to display
If I understand you, my inclination would be to map the unthresholded
volume with interpolated voxel.
Then map the thresholded volume with enclosing voxel. Then use Surface:
ROI to select metric =mythresh and draw an areal border around the
resulting cluster. Then render that border over
MFM, because it averages the intersection of the 12 PALS subjects, will appear
more smoothed than AFM. The range is likely to shrink.
Also, if you mean the range of your volume is wider than the range of either
AFM or MFM, then that could mean some of the extrema in your volume are outside
-B12.BOTH.JN97_03_With-Classes.73730.fociproj .
study_metadata_file Human.PALS-B12.LR.FOCI_JN97-03.study .
vocabulary_file Human.CorticalAreas.vocabulary .
vocabulary_file Human.Geography.vocabulary .
Donna
On Oct 9, 2013, at 10:09 AM, Donna Dierker do...@brainvis.wustl.edu wrote:
You're right
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Van: caret-users-boun...@brainvis.wustl.edu
[caret-users-boun...@brainvis.wustl.edu] namens Donna Dierker
[do
Weird. I'm curious: Have you tried loading another, existing metric file
before mapping (e.g., one that comes with the tutorial, or one you have mapped
previously)? It shouldn't matter, but I have seen other features under
Surface: Measurements fail, if an existing surface shape file was not
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