For mri_vol2vol try using --interp nearest
doug
Gabriel Go.Es. wrote:
>
> Yes, I did check the brainmask2raw.mgz, Im using brain2raw.mgz and/or
> brainmask2raw.gz to mask the rawavg.gz on the mri_mask. "mri_mask -T 2
> -keep_mask_deletion_edits rawavg.mgz brain2raw.mgz outbrain.mgz"
> And actually the brain.mgz and brainmask.mgz have values of one on
> edited voxels, but after mri_vol2vol or mri_convert -rl the voxel
> values appear with bigger values, and some of these values are like
> ventricles values, so I can not just put a high threshold; new values
> on edited voxels range from 1 to 40 approximately, and yes, the
> background has values less than 2.
> Gabriel
>
>
>
>
>
> > Date: Tue, 15 Mar 2011 13:30:40 -0400
> > From: gr...@nmr.mgh.harvard.edu
> > To: gabriel...@hotmail.com
> > CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu;
> ni...@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] mri_mask problem
> >
> > Have you checked brainmask2raw.mgz? It looks like you've checked
> > brain2raw.mgz, but you're not using it for some reason. Make sure the
> > background has values less than 2.
> > doug
> >
> > Gabriel Go.Es. wrote:
> > >
> > > 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
> > > > >>> Compliance
> > > > >>>>> HelpLine at
> > > > >>>>>> http://www.partners.org/complianceline . If the e-mail
> was sent
> > > > >>> to
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> > > > >>>>>>
> > > > >>>>
> > > > >>
> > > > >
> > >
> ------------------------------------------------------------------------
> > >
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> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> >
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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