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: greve@nmr.mgh.harvard.edu To: gabriellbk@hotmail.com CC: fischl@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu;
nicks@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: 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
> 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 >>> you in error >>>> but does not contain patient information, please contact the > sender >>> and properly >>>> dispose of the e-mail. >>>> >>
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