New subject: mri_mask problem

14 Mar 2011


      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: nicks@nmr.mgh.harvard.edu
To: gabriellbk@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: nicks@nmr.mgh.harvard.edu
To: gabriellbk@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: nicks@nmr.mgh.harvard.edu
To: gabriellbk@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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