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 >>>>> you in error >>>>>> but does not contain patient information, please contact the >>> sender >>>>> and properly >>>>>> dispose of the e-mail. >>>>>> >>>> >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer