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.
>>>>>>
>>>>
>>
>
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