Yes, I think Mike's approach is a good one also, although you have to be clear
about the somewhat different hypothesis you are testing
On Mar 22, 2012, at 9:15 PM, Michael Harms wrote:
>
> Hi Jeff,
> I personally like the idea of using average thickness as a covariate to
> control for a redu
Hi Jeff,
I personally like the idea of using average thickness as a covariate to
control for a reduction in "whole brain" thickness, and have used that
approach in a paper. If the Abstract that you mentioned indicated that
this is flawed, I'd be curious to know what the reason was...
cheers,
-MH
Hi Jeff
yes, I think this is still our recommendation for thickness, although
perhaps David Salat can verify. As far as surface area, you might get
Anderson Winkler to send you a preprint of his newly accepted paper on
surface area comparisons and how to do them properly. I would have said
no
Hi Jeff
<1 means compressed and >1 means expanded. You can take the log if you want
to turn it into the real line. I'm not sure age matters that much for the
white matter surface, although it would for the pial one
cheers
Bruce
On Thu, 22 Mar 2012, Jeff Sadino
wrote:
Hello,
Since the jac
Hello,
For cortical thickness normalizations, Bruce said not to normalize based on
a HBM abstract (
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html).
Is this still the consensus?
For cortical volume, it is pretty standard to normalize to eTIV.
For cortical surface area
Hello,
Since the jacobian files contain only positive numbers, is there any way to
make a distinction between a brain area that needs to be stretched bigger
to fit the template versus a brain area that needs to be squished smaller?
fsaverage is comprised of 40 subjects, but I wonder if the jacobi
Hello FreeSurfers,
I want to do several cluster-wise corrections at a p value of .1,
preferably in QDEC. To create the new "template cluster", I am using this
command:
mri_mcsim --o test --base mc-z --surf fsaverage lh --nreps 1 --fwhm 10
Is there a way that I can tell mri_mcsim to do a thres
did you run out of disk space? Does that path exist?
On Thu, 22 Mar 2012, Klein, Holger wrote:
Dear Freesurfers,
Command line: make_average_subject --out average --subjects ... (n=60)
.
.
.
.
.
Applying LTAtransformInterp (resample_type 1)
writing
to/Volumes/Macintosh/freesurfer/Kontrollen/
I'm dredging this 2 year old post up for the benefit of Google and anyone
else who wonders about the cause of this. It is a non-fatal error (for
FreeSurfer, but perhaps not other things) that is caused by having set the
variable:
POSIXLY_CORRECT=1
It causes bc (on Debian/Ubuntu) systems to fail
Dear Freesurfers,
Command line: make_average_subject --out average --subjects ... (n=60)
.
.
.
.
.
Applying LTAtransformInterp (resample_type 1)
writing to
/Volumes/Macintosh/freesurfer/Kontrollen//average/tmp/make_average_vol-tmp-15056/orig-A2/WE.mgh...
ERROR: failure writing
/Volumes/Macintosh/
Thanks for the quick answer :)
I'm not very familiar with cvs and was assuming 'stable' was only the name
of the directory in which the code would be checked out!
Thanks!
Nicolas
On Thu, Mar 22, 2012 at 3:09 PM, Nick Schmansky
wrote:
> the last arg should be 'dev', not 'stable'.
> > Hi all,
> >
the last arg should be 'dev', not 'stable'.
> Hi all,
>
> I followed the instructions on the wiki but it seems impossible to
> checkout
> the stable and release branches?
>
> [toor@linux:x86_64-Linux]...or/cvsroot/test$>cvs -d
> :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -
Hi all,
I followed the instructions on the wiki but it seems impossible to checkout
the stable and release branches?
[toor@linux:x86_64-Linux]...or/cvsroot/test$>cvs -d
:pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P -r
stable5 stable
cvs server: cannot find module `stable'
Hi everyone,
We had a last minute drop-out from our Boston FreeSurfer course which
takes place April 2nd through the 4th. If anyone is interested in taking
this spot, please let me know.
Details about the course content, the registration fee, and other
logistics can be found here:
http://surfer
Dear All
We want to find frontal
lobe grey and white matter volumes in a patient group to compare it
with control group. In particular, we want to see the grey and white matter
volumes in the dorsolateral prefrontal cortex (DLPFC). However
we seem to be
Hi all,
I'm currently compiling/installing freesurfer on mac osx lion, ubuntu
12.04 (will be relased soon) and lots of packages which are required by
freesurfer appear to be outdated.
Is there any step-by-step installation/compilation tutorial somewhere in
the web?
Therefore I have a couple of q
Hi Emily
yes, mri_surf2surf should do this for you.
cheers
Bruce
On Thu, 22 Mar 2012, Emily
Rogalski wrote:
> Hi All,
>
> Is it possible to resample a .sig file from a group thickness analysis in
> qdec so
> that the results could be displayed on a single subject's anatomy rather than
> the
Hi All,
Is it possible to resample a .sig file from a group thickness analysis in
qdec so that the results could be displayed on a single subject's anatomy
rather than the fsaverage anatomy in tksurfer?
Thanks,
Emily
--
Emily J Rogalski, PhD
Assistant Research Professor
Northwestern University
Hi Julia,
Are you editing on a Mac?
-Louis
On Thu, 22 Mar 2012, Richter, Julia wrote:
> Hi freesurfer experts,
>
> I am trying to correct the pial surfaces of my data. I was able to remove
> voxels with the right button of my mouse, but unfortunately, it didn't work
> out to add voxels. Can som
Hi Will,
I noticed this as well. I don't know Doug's thinking, but I suspect it
was just to avoid generating lots of files. The new script overwrites
the lh.seghead, when smoothing. I would just update your script to use
lh.seghead instead of lh.smseghead.
HTH
D
Will Woods wrote:
> Hi,
>
> I
Hi Julia
it's really hard to tell from just this image. If the problem is the
skull strip removing voxels you can use the "clone" tool to paint them
back in from another volume like the T1.mgz. Are you sure it's not dura or
pial vessels? Where in the brain do you mean?
cheers
Bruce
On Thu, 22
Hi Will
Doug is out of email contact until next week, and I suspect he's the best
one to help you. If you haven't heard by mid week can you repost?
cheers
Bruce
On Thu, 22
Mar 2012, Will Woods wrote:
> Hi,
>
> In my previous lab, which I no longer have access to, we ran
> mkheadsurf as part of
Hi,
I would like to use mri_robust_register to co-register
b-volumes to the reference b0-volume in a DTI dataset.
The documentation informs that it is not quite suitable
in case of large intensity differences which apply to
my case. How to proceed? Is a dev version available
for this purpose?
Che
Hi freesurfer experts,
I am trying to correct the pial surfaces of my data. I was able to remove
voxels with the right button of my mouse, but unfortunately, it didn't work out
to add voxels. Can somebody please help me with that? Do I need a middle button
on the mouse for it?
Attached you may
Hello,
I was running the tutorial on Qdec, when I went to generate stats data, it
started running fine, and then I got the following error message:
aparcstats2table --hemi rh --parc aparc.a2005s --meas area --tablefile
/mnt/hgfs/VBM/freesurfer_EONCS/EONCS/buckner_data/tutorial_subjs/qdec/stats
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