Hi Martin, I don't know as I don't use fslswapdim on a regular basis.
Sounds like the geometry is not being computed correctly in the new
file. In any event, it seems more like an fslswapdim issue that a
freesurfer one.
doug
Martin Kavec wrote:
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
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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