Hi Chris, I don't really see this as a problem for FreeSurfer or BBR as
much as it is a problem with FSLView not being able to re-orient images
so that they don't show up upside-down. If you have two matrices (one to
convert to T1 space, the other to the reoriented space), you can merge
the mat
Hi Noam, sorry, this one slipped through the cracks (would not have seen
it except for Chris' email today). The problem with your data is not
that the brain is upside down but that the letters (AP, LR, SI) are not
appropriate. I just tried this procedure on my data and could not
replicate this
Hi,
I have run into the same problem. I have managed to partially diagnose
it, got some workarounds, but no real solutions. I would greatly
appreciate FreeSurfer team for some feedback.
So it's all about orientations. FreeSurfer internally uses LPI and FSL
(Especially FSLView) uses RAS. Try conver
Can you send a pic?
noam Schneck wrote:
> Nevertheless when I use that register.dat to view a statmap on the
> anatomical space (which is the same registration from epi to t1 space)
> I have activation outside of the brain. I understand that BBR has
> aligned the images well, but it seems not t
That registration appears to be ok. Remember, that is the boundary
between the cortical gray and white matter, not the edge of the brain or
skull, so it should be interior.
doug
noam Schneck wrote:
> Here are slices from the registration.
>
> On Wed, Aug 31, 2011 at 2:39 PM, Douglas N Greve
>
You should not need to adjust the registration. The surface should
follow the gray white boundary in the EPI (hard to see but there). Can
you send a pic of the green surface on the EPI with the default
registration (ie, without you making changes)?
noam Schneck wrote:
> It is from an individual
It is from an individual. I checked the registration, the green surface
outline seems well within the movable EPI image. I can scale it down
manually and than the zstat, with the scaled down register.dat, fits within
the anatomical. Is this the only solution?
On Wed, Aug 31, 2011 at 2:34 PM, Dougl
Is this a zmap from the individual run or the gfeat? If individual,
double check the registration with
tkregister2 --mov example_func.nii.gz --reg anat2exf.register.dat --surfs
If from a gfeat, then you should use anat2std.register.dat, like
tkmedit bert orig.mgz -overlay zstat1.nii.gz -overlay
noam Schneck wrote:
> Hi Doug
>
> Here are more detailed versions of my first two questions.
>
> 1) I used tkmedit to look at the mean_func produced by a gfeat
> analysis of one subject's three functional runs overlayed onto the
> anatomical image produced by recon-all on that same
> subject(
Hi Doug
Here are more detailed versions of my first two questions.
1) I used tkmedit to look at the mean_func produced by a gfeat analysis of
one subject's three functional runs overlayed onto the anatomical image
produced by recon-all on that same subject(bert/mri/orig.mgz). The
registration mat
Hi Noam,
noam Schneck wrote:
> Hi,
>
> I am trying to use reg-feat2anat to register my Feat analyses to
> anatomical images and running into a number of problems.
>
> 1) When I check the registration of the mean_func to the anatomical in
> tkregister2 it looks fine. But when I overlay the fsl s
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