Hello Bruce and Nick, I've tryed these options you said and still not works, 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: fis...@nmr.mgh.harvard.edu
> To: gabriel...@hotmail.com
> CC: ni...@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: 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
> >>>>>>> _______________________________________________
> >>>>>>> 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
> >>> to
> >>>>> whom it is
> >>>>>> addressed. If you believe this e-mail was sent to you in error
> >>> and
> >>>>> the e-mail
> >>>>>> contains patient information, please contact the Partners
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> >>>>> HelpLine at
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> >>>>>>
> >>>>
> >>
> >
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