Hello,
I am trying to verify the wmparc.mgz segmentations. I have identified
outlier regions statistically, but then when I load up the wmparc.mgz file
to QA visually, I find it is very difficult to QA the white matter regions.
The problem is that because there is no contrast in the white matter
replace http with ftp, and it should work.
n.
> Hi,
>
> When I try to download v4.5.0 (Mac version) from the Archive, it seems
> like
> the file is missing/unavailable?
>
> http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.5.0/freesurfer-Darwi
> n-leopard-i686-stable-pub-v4.5.0-full.dmg
>
Hi,
When I try to download v4.5.0 (Mac version) from the Archive, it seems like
the file is missing/unavailable?
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.5.0/freesurfer-Darwi
n-leopard-i686-stable-pub-v4.5.0-full.dmg
Have also tried the mirrors link but that is down also.
Could s
Hi Lin,
that is under development. We don't have anything we are ready to
distribute at this time. Hopefully within the next year though.
cheers
Bruce
On Mon, 20
Dec 2010, Lin Nga wrote:
> Hi all,
>
> Please excuse my naive question; I am new to FreeSurfer. I am trying to
> segment amygdala su
Hi all,
Please excuse my naive question; I am new to FreeSurfer. I am trying to
segment amygdala subregions and can't quite figure out how to do this. I
didn't find anything in the tutorials or the freesurfer archives; if there
is any documentation on how to do this, could someone point me in the
Hi there,
When I am using the "tksurfer" command for visualization, I only get a
black screen:
tksurfer $subject rh inflated
There is no error reported at the command prompt except for a warning:
No colortable found!
Here is the version of the freesurfer I am using:
freesurfer-Linux-centos4
Then I am not doing the question propperly, and I obviously did not
understand the basis of tksurfer :)
I am going to work in Matlab, and I just wanted to use the output of
Freesurfer to help me with my algorithm, so I am not going to use neither
tkmedit nor tksurfer. Hence, I do not exactly need
Hi Fidel
the surfaces of the same hemi for a given subject area all topologically
equivalent and share an index structure. what that means is that the
vertex label/annotation can be shown/used on any surface, including the
?h.white and ?h.pial surfaces (which is probably what you want). Or you
Thanks mr Fischl, but these surfaces are a deformation of the original
brain (According to what I have read in the wiki). My intention is to
write an algorithm to do some operations on the original images, using the
sulci information from freesurfer. In order to do that, I would need the
sulci info
Hello Freesurfers,
We are beginning to perform QC on our subjects and want to look at
signal to noise ratio. I've taken a look at the fsnr.nii overlay
files, but we would like to be able to calculate a whole surface
value for SNR for each functional run of each subject, so that we can
exclude
the gyral/sulcal segmentations are generated on the surfaces and viewable
in tksurfer. For example:
tksurfer lh inflated -aparc
will bring up and show the lh.aparc.annot on top of the inflated
surface. You can also load them from the tksurfer interface using
file->label->import annotation
c
Hi,
I am pretty new in freesurfer and I do not know if this question has been
answered before (It is difficult to search for 1 basic question), so I
will post it anyways:
- Is there any segmentation/labeling in freesurfer that allows the user to
identify all the sulci of an MR image? I have done
probably. The T2* will be different, so you'll have a different TE and
different contrast, SNR and CNR
On Mon, 20 Dec 2010, Anthony Dick wrote:
> Would this problem also apply for fMRI or diffusion weighted scanning?
>
> On 12/20/10 10:41 AM, Bruce Fischl wrote:
>> Hi Anthony,
>>
>> I don't thin
Would this problem also apply for fMRI or diffusion weighted scanning?
On 12/20/10 10:41 AM, Bruce Fischl wrote:
> Hi Anthony,
>
> I don't think so. The problem is that the fundamental T1 contrast is
> different at 3T than att 1.5T, which results in systematic biases.
>
> cheers
> Bruce
> On Mon,
Hi Anthony,
I don't think so. The problem is that the fundamental T1 contrast is
different at 3T than att 1.5T, which results in systematic biases.
cheers
Bruce
On Mon,
20 Dec 2010, Anthony Dick wrote:
> This is just a thought, but is this issue mitigated to some degree if
> you can show that
This is just a thought, but is this issue mitigated to some degree if
you can show that the regions in which you are interested meet a certain
minimum signal to noise ratio? Or maybe a more stringent requirement
would be necessary, such that the SNR of the ROIs don't differ
significantly?
Alwa
Hi Diederick,
In a longitudinal study you need to ensure identical acquisition and
processing, else you'll introduce a systematic bias.
Some of my recent analyses indicate that even updating the software on the
scanner can bias your results. Hardware changes are worse.
Best Martin
On Dec 20,
Dear all
I am using the tkmedit GUI to add/erase pixel in a slice-wise fashion in order
to subsequently apply a tessellation on the white matter.
I launch the command
cd subject/mri
tkmedit -f brain.mgz -aux wm.mgz
from linux shell (64bit CentOS), where brain.mgz is the anatomical MRI and wm
is
Dear Diederick,
were all subjects acquired at point 1 with 1.5T and at point 2 with 3T? Or
was the same subject acquired with the same scanner at both timepoints? In
the first case, could it be simply a problem of scanner-related variability
of ICV assessment (different scanner different seque
Hi all,
I have a dataset with AD patients that were scanned twice, once at 1.5T and
once at 3T at an interval of a few years. The ICV values are lower for almost
all subjects at timepoint two (FS 5.0). Isn't ICV in the later FS versions
supposed to be independent of brain volume as it is based
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