Helo Bruce, I've tryed these options you said and still not working, I must say that is not in all my subjects,
I've tryed both brain.mgz and brainmask.mgz.
The commands I've used are:
A1) mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheader A2) mri_mask flag -keep_mask_deletion_edits rawavg.mgz brain2raw.mgz outbrain.mgz
after mri_vol2vol the brain2raw.mgz look perfecty fine, but when apply the mri_mask the image apperars with no edits.
B1) mri_convert -rl rawavg.mgz brainmask.mgz brainmask2raw.mgz B2) mri_mask flag -T 2 -keep_mask_deletion_edits rawavg.mgz brainmask2raw.mgz outbrain2.mgz
I've ran the mri_mask command with and without the -keep_mask_deletion_edits flag and again appears to be the mri_mask command the one that is not doing the work, actually the outputs from mri_convert and mri_vol2vol, looks pretty similar, any ideas?
Bests Gabriel
Date: Mon, 14 Mar 2011 08:57:16 -0400 From: fischl@nmr.mgh.harvard.edu To: gabriellbk@hotmail.com CC: nicks@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_mask problem
Hi Gabriel,
did you convert the brain.mgz so it is in the same space as the rawavg.mgz using either mri_convert -rl or mri_vol2vol? If so, you can try mri_mask -t <threshold>. The default is 1e-10 so pretty much anything non-zero is dept. Try changing it to 2 (voxels edited to be turned off are 1).
cheers Bruce
On Mon, 14 Mar 2011, Gabriel Go.Es. wrote:
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 >> _______________________________________________ >> 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
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