Hi Dough,
I took another subject, which was analyzed recently with the latest FS and the result of the masking is gook!
I found another issue in my experimenting!
Here is exactly what I did: 1. mri_convert -i brainmask.mgz -o brainmask.nii.gz 2. fslswapdim brainmask.nii.gz x z -y brainmask.axial.nii.gz (reslice to axial)
Now when I load brainmask.mgz (or brainmask.nii.gz) and brainmask.axial.nii.gz to tkmedit there is a 1 voxel shift in inferior to superior direction.
Can you reproduce that and do you know where it comes from?
Thanks,
Martin
On Monday 06 April 2009 23:13:48 Doug Greve wrote:
but you are using aparc+aseg to generate the mask, so if aparc+aseg is perfect, the mask should be as well. Do the mask and aparc+aseg match?
On Mon, 6 Apr 2009, Martin Kavec wrote:
Doug,
ribbon (aparc+aseg) looks perfect, and corresponds to the surfaces ?h.white.
Thanks,
Martin
On Monday 06 April 2009 22:17:18 Doug Greve wrote:
I thought it was 4.0.3, so maybe that's not it. Can you look at the ribbon.mgz file? You can load it as a segmentation, ie,
tkmedit subject orig.mgz -seg ribbon.mgz
aparc+aseg is suppossed to inherit the cortex from ribbon.mgz
doug
On Mon, 6 Apr 2009, Martin Kavec wrote:
Hi Dough,
this data were analyzed using 4.0.4. So indeed it not the latest, which I am running normally. From which version has this been fixed, so I can check, before re-runing. From which point should I rerun the analysis.
Thanks,
Martin
On Monday 06 April 2009 18:42:36 Douglas N Greve wrote:
This looks like a problem we had with an older version. What version of freesurfer are you running?
Martin Kavec wrote:
Hi,
I am trying to mask a non-brain tissue left by watershed based on the cortical surfaces. I found that all what I need to be left is in aparc+aseg.mgz, so I converted it to nifiti, along with brainmask.mgz and used FSL to binarize aparc+aseg and mask the brainmask. I found that at many places the results is too conservative and too much of the GM is missing, see the attached images, and particularly the temporal lobes.
Is there a better approach to what I am trying to do and what could be the explanation to the results I get.
Thanks,
Martin