Hello,
Thank you Nick, Martin, and Doug for your previous feedback about ICV.
I have a couple more questions that I am hoping you could clarify for
me.
To verify my ICV value, some pages on the mailing list and wiki say to
use this command:
tkregister2 --s subject --fstal --surf
Other places sa
Hello.
Instead of using Freesurfer's averaged brain in qdec, I ran the following
command to create an average of our participants:
recon-all -s [subject] -qcache target avgsub
While running, it reported the following for every subject:
Error: could not open file
"/Users/Tiana/ucr_freesurfer_da
hmmm, could also be a low sensitivity region if the region around the eyes
doesn't have coil coverage. I would try putting a line of control points in
the white matter going from anterior and moving posteriorly until the
drop-off is not that big (i.e. until the T1.mgz has voxels==110 in the
whi
Hi,
No problem - thanks for coming back to me.
Imaging was carried out with a GE Excite II 3-T scanner using an eight-
channel phased array coil. We acquired coronal 3D-T1 weighted fast spoiled
gradient echo (FSPGR) (0.94 × 0.94 × 1.1 mm) which is what I am plugging
into Freesurfer.
There is act
Hi Mahinda,
sorry, I meant to respond to this. It's hard to tell from the image - is
there actually data in the frontal regions? What is the source of the
drop-off? Is it a slab selective acquisition and is anterior/posterior the
slab direction?
cheers
Bruce
On Mon, 23 Jan 2012, Mahinda Yo
Dear Experts,
Sorry if this is a repost, but I was not sure it got posted.
I have a few subjects that I want to salvage and use where there appears to
be significant signal inhomogeniety in the last few frontal slices (see
T1.mgz in attached figure 1). Despite the use of control points (placed
w
Hi Doug,
I spoke too soon. I tried to follow your advice and run either command:
In a terminal, cd to the GLM directory inside qdec directory and then cd to the
folder of the contrast of interest and run
mri_segstats --id 1 --slabel fsaverage lh yourlabel --i gamma.mgh --sum
yourlabel.sum
t
Antonella Kis wrote:
> Hi,
>
> I would like to do a Group Analysis for my FA data.
>
> For all my subjects (controls + patients) I have all the
> fa-masked.ANAT+CVS-to-avg35.mgz (the resampled registered image to CVS
> space).
>
> I am not sure if my steps for the Group Analysis are the right o
Hi,
I would like to do a Group Analysis for my FA data.
For all my subjects (controls + patients) I have all the
fa-masked.ANAT+CVS-to-avg35.mgz (the resampled registered image to CVS space).
I am not sure if my steps for the Group Analysis are the right one:
1) Concatenate FA from individuals
Hi Yuko, it should be performing Gaussian Random Field (GRF)
cluster-wise correction. Based on the smoothness, the size of the search
space, and the voxel-wise threshold, it attempts to compute the p-value
of resulting clusters. The differences between GRF and doing the
simulation are that GRF
Hello Experts,
I am analyzing cortical thickness of two groups (APOE 4carries vs. noncarriers)
in freesurfer with age as a co-variate.
I am uncertain about the statistical differences behind:
1)Does the correlation between thickness and age accounting for APOE, differ
from 0?
in contrast to
On 1/23/12 08:17 , octavian lie wrote:
> Thank you for the info, can you share what freesurfer version you
> have that happens to work well with ubuntu 11.10?
> Octavian
>
The lastest stable works... as well as the development versions. There
is sometimes a library version error which is easily f
Thank you for the info, can you share what freesurfer version you have that
happens to work well with ubuntu 11.10?
Octavian
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