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
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
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
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
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
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
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
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
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
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
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.
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
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
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