External Email - Use Caution
Hi Eugenio,
Thank you for your reply. The solution to blend the two segmentation will
work for me.
If you could share the Matlab code that would be great.
Also one other related question i have is related to edits and
brainstem-structures.
1. The first time i run recon-all, i use: "recon-all -all -s bert
-brainstem-structures.
2. Then suppose, I add control points or edit brain-mask; i re-run
recon-all with:
3. recon-all -s bert -autorecon2-cp -autorecon3
1. when i do this i think i should also add the brainstem-structures
flag again. thus my command will be:
4. recon-all -s bert -autorecon2-cp -autorecon3 -brainstem-structures.
Does step-4 look correct to you ?
Thanks
Mehul
On Thu, Jun 21, 2018 at 2:44 AM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:
> Dear Mehul,
>
> Yes, the labels from the Brainstem module overlap with the definition of
> ventral-dc in aseg.mgz, since they are based on atlas built with
> delinations made with different criteria.
>
> A trick you can use to blend the two segmentations into one is:
>
> 1. Create a binary mask for the whole brainstem using
> brainstemSsLabels.v10.FSvoxelSpace.mgz.
>
> 2. In aseg.mgz (or aparc+aseg.mgz), replace the label of every voxel in
> the mask by that of the nearest voxel outside the mask.
>
> 3. Paint the brainstem from brainstemSsLabels.v10.FSvoxelSpace.mgz over
> the mask in the output of step 2.
>
> Does this make any sense? I can provide you with some Matlab code if you
> with.
>
> Cheers,
>
> /E
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: *Mehul Sampat <mpsam...@gmail.com>
> *Date: *Thursday, 21 June 2018 at 04:10
> *To: *Freesurfer Mailing List <Freesurfer@nmr.mgh.harvard.edu>, "Iglesias
> Gonzalez, Eugenio" <e.igles...@ucl.ac.uk>
> *Subject: *Merging aparc+aseg.mgz and brainstemSsLabels.v10.
> FSvoxelSpace.mgz
>
>
>
> Hi Eugenio and Bruce,
>
>
>
> We used freesurfer-6.0.0 to segment the brain-stem into different
> different structures.
>
>
>
> I see we get two mgz files after this process:
>
> aparc+aseg.mgz and brainstemSsLabels.v10.FSvoxelSpace.mgz
>
>
>
> Do you have any recommendations to combine these two masks into a single
> mask ?
>
>
>
> I see pons in brainstemSsLabels.v10.FSvoxelSpace.mgz overlaps with the
> brain-stem in aparc+aseg.mgz but the midbrain in
> brainstemSsLabels.v10.FSvoxelSpace.mgz
> overlaps with brain-stem and the ventral-dc in aparc+aseg.mgz.
>
>
>
> Any recommendations are appreciated.
>
> Thanks
>
> Mehul
>
>
>
>
>
>
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
