Hello Nick
I'm wondering if you're able to verify my data today,
I did try using brainmask.mgz to mask the rawavg.mgz, and didn't worked,
I'm guessing you'll need my data, to see if there is something wrong on it, but
I think is gonna be hard to send it to through the e-mail.
Bests,
Gabriel.
> Subject: RE: [Freesurfer] mri_mask problem
> From: ni...@nmr.mgh.harvard.edu
> To: gabriel...@hotmail.com
> Date: Thu, 10 Mar 2011 21:38:50 -0500
>
> i'd have to try to replicate this myself, although it will have to wait
> till monday (i'm with the freesurfer group three days a week).
>
> i wonder if you can use the brain.mgz as your mask instead of
> brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels but their
> actually not there (zeroed).
>
> n.
>
> On Thu, 2011-03-10 at 08:42 +0000, Gabriel Go.Es. wrote:
> > Hello Nick,
> > good mornig for you, when you read this, Now I have tryed the flag in
> > the mri_mask command but it seems too similar to what was doing
> > before, it says that will transfer 1 voxel edits to dst vol, but there
> > many more voxels edited, I have also tryed mri_vol2vol in the
> > brainmask.mgz intead of brain.mgz but the result is exactly the same
> > (the output from mri_vol2vol has the voxel 'deletions', but the
> > mri_mask ignore them. Now i have no idea how to solve this, do you?
> >
> > Bests,
> > Gabriel
> >
> >
> >
> >
> >
> >
> >
> > > Subject: RE: [Freesurfer] mri_mask problem
> > > From: ni...@nmr.mgh.harvard.edu
> > > To: gabriel...@hotmail.com
> > > Date: Wed, 9 Mar 2011 18:00:37 -0500
> > >
> > > we've improved some of the help text for the next version (5.1),
> > which
> > > is the only reason i noticed it this time.
> > >
> > >
> > > On Wed, 2011-03-09 at 22:58 +0000, Gabriel Go.Es. wrote:
> > > >
> > > > Than you Nick,
> > > >
> > > > Actually that was exactly what i did, delete some voxels from the
> > > > brainmask, I will try adding the flag and let you know, I dind't
> > saw
> > > > that this option exist in the mri_mask.
> > > >
> > > > thank you again,
> > > > Gabriel
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > > Subject: Re: [Freesurfer] mri_mask problem
> > > > > From: ni...@nmr.mgh.harvard.edu
> > > > > To: gabriel...@hotmail.com
> > > > > CC: freesurfer@nmr.mgh.harvard.edu
> > > > > Date: Wed, 9 Mar 2011 17:52:34 -0500
> > > > >
> > > > > hi, not sure what you are trying to do, as the commands below
> > seem
> > > > to do
> > > > > what i expect them to do, which is to create a masked
> > > > (skull-stripped)
> > > > > version of rawavg.mgz. what do you mean by 'manual segmentation
> > > > > changes'?, and what exactly is going wrong?
> > > > >
> > > > > if you deleted voxels in brainmask.mgz, then perhaps you need to
> > add
> > > > the
> > > > > flag -keep_mask_deletion_edits to mri_mask to transfer those
> > voxels
> > > > > ('deleted' voxels actually have a special value to indicate
> > > > deleted).
> > > > >
> > > > > n.
> > > > >
> > > > >
> > > > >
> > > > > On Wed, 2011-03-09 at 22:28 +0000, Gabriel Go.Es. wrote:
> > > > > >
> > > > > > Hello everybody,
> > > > > > Sorry for the insistance, but I need to solve this...
> > > > > >
> > > > > > I'm making some manual segmentation changes in the
> > brainmask.mgz
> > > > and
> > > > > > using mri_vol2vol and mri_mask commands to apply these changes
> > to
> > > > the
> > > > > > rawavg.mgz, the output from the mri_vol2vol looks perfectly
> > > > normal,and
> > > > > > retains all changed made by me, but when I use the mri_mask
> > > > command
> > > > > > over the rawavg.mgz no segmentation seems to be donne in the
> > final
> > > > > > output file.
> > > > > >
> > > > > >
> > > > > > Does any one has an idea of what could be wrong?
> > > > > >
> > > > > >
> > > > > > the commands after manual corrections are:
> > > > > >
> > > > > >
> > > > > > mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out
> > brain2raw.mgz
> > > > > > --regheader
> > > > > > mri_mask rawavg.mgz brain2raw.mgz outbrain.mgz
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > Thanks in advanced,
> > > > > > Gabriel
> > > > > > _______________________________________________
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> > > > >
> > > > >
> > > > >
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