Not sure it's helpful.
The simplest way I can think of is to directly edit WM.mgz. You can load
wm.mgz into matlab, it's basically a 3D matrix. You can directly set
values for wm matrix, for instance
wm(wm(:)>200)=110;
Then you save the new wm matrix into wm.mgz.
On 9/5/16 10:54 AM, Benja
Hi Ben
sorry, but I don't know how to fix it automatically. You have voxels that
look just like wm in the gm - that's going to be tough to avoid. You could
try messing with some of the mris_make_surfaces options, but I don't have
much confidence that it will help.
Any idea why you are gettin
Hi Bruce and Clara,
Many thanks for your comments. Indeed the bright points are segmented as WM
in wm.mgz, however these errors do not occur only in a few places but in
many slices throughout the brain so manual edits will be very extensive,
which is why we wanted to double check that there is no
If the T2 is already high-res, and having already the T1, I don’t think that
the FLAIR would help much.
Cheers,
/E
Juan Eugenio Iglesias
Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 5 Sep 2016, at 16:22, V
Sorry, but a 3-channel segmentation is not part of the future FS6.
Juan Eugenio Iglesias
Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 5 Sep 2016, at 15:54, Jovicich, Jorge
mailto:jorge.jovic...@unitn.it>>
Dear Jorge,
In my case I am using either T1+T2 or T1+FLAIR.
I had no intention of using all three at once, but now I am also wondering
if this would be an improvement.
Cheers,
Renata
On Mon, Sep 5, 2016 at 4:54 PM, Jovicich, Jorge
wrote:
> Hi Eugenio,
>
> just to confirm I understand the curr
Hi Eugenio,
just to confirm I understand the currently available options. There are
two multispectral strategies (MPRAGE + high res 2D T2, or MPRAGE + 3D
FLAIR). It would be great to see if the combo option improves things
even further for the subfields (MPRAGE + high res 2D T2 + 3D FLAIR). Is
The same one; just change the input file and the analysis ID
- T2: recon-all -s mySubject -hippocampal-subfields-T1T2 myT2scan.nii.gz
T2
- FLAIR: recon-all -s mySubject -hippocampal-subfields-T1T2 myFLAIRscan.nii.gz
FLAIR
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior Research Fellow
Dear FS experts,
I have a question about the "segmentation with an additional scan -
multispectral segmentation"
on the hippocampal sf segmentation, FS dev. 6.0.
For controls on which I had already run recon-all -all, I added the T2
sequence with the following
command:
recon-all -s \
-hippocam
