Dear FreeSurfer Experts,
I'd like to know how to measure the volume of a brain region using freesurfer.
I know to obtain the volumes after runnin recon-all command. But I don't find
the brain volume of my interest which is DLPFC.
How can I get the brain volume of my interest.?
Thanks for your r
Ah, OK, makes sense - should have guessed, sorry, vol2surf behaved so agreeably
with the vertex-free mask!
Shall make that surf mask now, thanks much,
Fred
On 14 Apr 2013, at 22:56, Douglas Greve wrote:
>
> Oh, the label should be a surface label. mri_cor2label creates a volume label
> (b
Oh, the label should be a surface label. mri_cor2label creates a volume
label (basically it just means that each label point corresponds to a
1mm3 cube instead of a verex -- the vertex numbers should all be -1).
Try running vol2surf on the mask (using nearest interp) to create a
surface mask.
Mike,
We dont have a RHEL 5.9 system to replicate the issue. However, I did
find a bug in qdec where the 'Min' value in the Threshold settings would
not update the display when a value was entered. This bug was
introduced when the 'Mid' value was removed (which is why I think the
v5.1 qdec works
Hi Doug
I've actually tried both inclusive and exclusive and have failed - just checked
again in tkmedit that the label was coming up correctly and it was.
Just to double-check - the label should be in the space of the --mov, right?
Thanks!
Fred
Hi Fred, that mask is an inclusive mask, no
Hi Fred, that mask is an inclusive mask, not an exclusive mask. Try
inverting you mask.
doug
On 4/14/13 4:31 PM, Fred Dick wrote:
Dear all
I am painting some higher-res anatomical data from a volume to a
surface, and want to use a mask that excludes the vessels. (The same
data but 1x1x1 c
Dear all
I am painting some higher-res anatomical data from a volume to a surface, and
want to use a mask that excludes the vessels. (The same data but 1x1x1
conformed were used to create the surface).
I've created a binary label in the same space
>> mri_cor2label --i ./R2Mask.nii.gz --l ./R
Sorry about my previous email, it seems I downloaded it three times, it is
installing ok now...
On Sun, Apr 14, 2013 at 8:02 PM, Garikoitz Lerma-Usabiaga <
gariko...@gmail.com> wrote:
> I cannot download it, do you think the problem is on my side?
>
> Terminal paste:
>
>
> Last login: Wed Apr 10
1) You can use mri_surf2surf to map data from an individual subject to
our normalized (fsaverage) coordinate system.
2. Not sure what this means. In fsaverage space there really is no
volumetric coordinate for a vertex, just it's location on the sphere. For
individual subjects you can compute
I cannot download it, do you think the problem is on my side?
Terminal paste:
Last login: Wed Apr 10 22:01:36 on ttys000
iMacGari2:~ gari$ curl -O
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0/freesurfer-Darwin-lion-stable-pub-v5.2.0.dmg
% Total% Received % Xferd Average Spee
I had several problems testing freesurfer 5.2 installation, as
previously posted. Now it is all OK and I would like to share what I
could learn:
1- It does not work on Fedora 18 (segfaults with all tests with tkmedit,
tksurfer and recon-all) that is due to a restriction imposed by glibc
(only new
Hi Marie,
no, that won't account for variability across slices in the l/r
direction. Try rerunning mri_cc with -t 0 (thickness) and see if it
generates a cc in just the midsagittal plane
cheers
Bruce
On Sun, 14 Apr 2013, Marie Schaer wrote:
>
> Hi Bruce,
>
> Thanks for your response. Then I
Dear prof. Bruce
Thanks once again. As you clarify that each brain has different number of
vertices. But still I want to ask the followings:
1) How to map these on some standard template say Freesurfer template and
then retrieve cortical thickness for each vertices?
2) How to identify the locati
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