I wanted to bump this:
I have license errors with FS 5.3 that don't appear for
equivalently-configured FS 5.1 and FS 4.5 installations. How shall I
troubleshoot?
SYMPTOMS:
$ mri_convert $FREESURFER_HOME/subjects/bert/mri/T1.mgz T1.mgz
mri_convert
Hi Lisa
globus pallidus is included in the aseg, have you looked at it? The
others you could lab on the fsaverage volume and warp to individual
subjects if you want, but that won't be as accurate as including them in
our atlas (but a lot easier!). We are working on segmenting things like
you need to run autorecon3 also
On Wed, 4 Sep 2013, Miggy Chuapoco wrote:
Hi Bruce,
I was able to change the white matter label values to 255 and the rest to 1
however when I ran -autorecon2-wm the new surface looks the same as the old
when I view them both in tksurfer. Should I be running
Hi,
Thanks for all the replies, I solved the problem I had before.
However, after finishing the Tracula pre-processing steps I tried to
visualize the tracts by typing:
freeview -tv CTR01/dpath/merged_avg33_mni_bbr.mgz
And, as you can see in the picture I'm attaching to this email, it seems
the
A. You should overlay the tracts on the subject's FA (see example command line
on wiki)
B. Check the mailing list archives about reinitializing tracts. That should
improve the results here. You don't need to reinitialize the tracts that are
already correct (although none of yours look
Hi Christopher,
Thanks a lot for such a prompt reply.
I know I should overlay the tracts of the FA image, but I just wanted to
show you how small the reconsctrutions were.
I don't think this is particularly noisy data.
I'm trying to find solutions on the mailing list archives by typing
Try this:
http://www.mail-archive.com/search?q=reinitl=freesurfer%40nmr.mgh.harvard.edu
From: Joana Braga Pereira [jbragapere...@gmail.com]
Sent: Thursday, September 05, 2013 9:51 AM
To: Watson, Christopher
Cc: Anastasia Yendiki;
Thanks, Bruce and Doug; this raises other questions for me about
mris_make_surfaces, but I'll ask those in a new thread.
Thanks again,
David
On Wed, Sep 4, 2013 at 5:59 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
no, the smoothing is done irrespective of the intensity volume (in
what does a slope of Sex mean? Is Sex a continuous variable?
On 09/05/2013 11:03 AM, Yang, Daniel wrote:
Hi Doug,
So I have two variables: Diagnosis (patient vs. control) and Sex
(female vs. male).
My model would be:
cortical thickness = intercept + (slope1 * Diagnosis) + (slope2 *
Hi Doug,
So I have two variables: Diagnosis (patient vs. control) and Sex (female vs.
male).
My model would be:
cortical thickness = intercept + (slope1 * Diagnosis) + (slope2 * Sex).
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Hi all,
I have two questions:
1. Does tkmedit, or freeview work under VirtualBox
2. Is it possible to parcelate white matter in freesurfer?
Thanks,
Martin
Sent from my iPad
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Hello everyone,
I am trying to gather the curvature (of a frontal ROI created through
mri_mergelabels) through mris_anatomical_stats using the following
mris_anatomical_stats -l 1220/label/lh.frontalmerge.label -f frontal_table 1220
lh pial
The table produced doesn't upload well into a
Hi everyone,
I would like to produce lh.white, lh.area, and lh.curv files of the type
produced by mris_make_surfaces, but where the input is a mask of the left
hemisphere white matter alone.
Specifically, suppose I start with the file lh.wm-mask.nii and use
mri_convert to make lh.wm-mask.mgz.
Hm, this looks uniformly bad. Have you checked that the gradient
directions are correct? You can check that by looking at the eigenvectors
from the tensor fit that's done as part of the preprocessing. Although
tracula doesn't use tensors for tractography, it's a quick way to check
that your
Hi Martin
1. Yes, I think people have done this.
2. Yes, we automatically generate a white matter parcellation and store
it in the volume wmparc.mgz
if you have diffusion data you can check out Anastasia Yendiki's
excellent TRACULA tool.
cheers
Bruce
On Thu, 5 Sep 2013, Martin Kavec
wrote:
Thanks a lot for this positive news!
Cheers,
Martin
Sent from my iPad
On 5.9.2013, at 17:49, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Martin
1. Yes, I think people have done this.
2. Yes, we automatically generate a white matter parcellation and store it in
the volume
Thanks!
I will try that and let you know!
joana
2013/9/5 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Yes, it does look from the images like the L-R and A-P directions are
swapped. So you can switch around the x and y columns of you gradient table
and rerun the preprocessing and check
Yes, it does look from the images like the L-R and A-P directions are
swapped. So you can switch around the x and y columns of you gradient
table and rerun the preprocessing and check the eigenvectors again. It may
be some other combination of swaps that needs to be done, but the x and y
Hello Freesurfers,
I am re-running an older analysis in stable3. I know that this version
is out of date, but I'm trying to line up new data with old data. I
have previously run a script that uses the func2roi-sess command with
no problems. Now, when I run the same script, I'm getting a new
I don't understand what you have done. Can you elaborate?
On 09/05/2013 04:45 PM, ye tian wrote:
Dear Freesurfers,
I compared my QDEC and glm (command line) results, using the same
contrast and threshold, but the size of the red cluster (barely
visible on glm) is quite different. Is this a
Dear Doug,
Sorry! I just realized that I selected the wrong question from QDEC. Never
mind about this question.
Thank you so much for asking me to elaborate the procedure.
Sincerely,
Ye
On Thu, Sep 5, 2013 at 4:11 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
I don't understand what
Hi Jeff, func2roi-sess is obsolete (should not have included it in 5.3).
You need to use a combination of funcroi-config and funcroi-sess. See
the help with funcroi-config
doug
On 09/05/2013 03:45 PM, jwa...@nmr.mgh.harvard.edu wrote:
Hello Freesurfers,
I am re-running an older
Indeed, they look like they're oriented A-P in the corpus callosum and L-R
in the cinglulum, when it should be the opposite obviously. This'd mean
you'd have to swap things in the gradient table. It's hard to tell for
sure from the screenshot though. If you upload the dtifit_FA and dtifit_V1
Sex is a nominal variable but can be coded as 0,1.
If it's coded as 0 (male), 1 (female); then the slope means, independent of
Diagnosis, how much thicker the brain the female (vs. male) is.
But if I model Sex as a nominal variable, there is always an interaction term
between Diagnosis and Sex
This is treating Dx and Sex as a continuous variable. I've never seen it
done before and don't recommend it, but if you want to do it, set up a
FSGD file with one group (eg, Main) and two variables. See the FSGD page
on the wiki
doug
On 09/05/2013 03:04 PM, Yang, Daniel wrote:
Sex is a
You could probably load them in matlab and compare there.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of David Romano
[drom...@stanford.edu]
Sent: Thursday, September 05, 2013 8:01 PM
To:
Try mris_diff
doug
On 9/5/13 8:01 PM, David Romano wrote:
Hi everyone,
I'm trying to figure out whether two surfaces which appear identical
in freeview are indeed identical. Using diff shows the files are not,
but since they're binary, I can't tell whether this difference is
simply due to
Dear Bruce,
Is globus pallidus in aseg named pallidum, as I only see this?
For labeling the regions, should I do the following steps, please correct if I
am wrong.
1. use tkmedit to draw the region on fsaverage question: should these regions
be drawn as segmentation or label?
2. then use
Thanks, Doug! -David
On Thu, Sep 5, 2013 at 6:43 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote:
Try mris_diff
doug
On 9/5/13 8:01 PM, David Romano wrote:
Hi everyone,
I'm trying to figure out whether two surfaces which appear identical in
freeview are indeed identical. Using
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