[Freesurfer] mri_mask problem
Hello, 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 --regheadermri_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] mri_mask problem
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 --regheadermri_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.
Re: [Freesurfer] mri_mask problem
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 +, 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
___
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.
Re: [Freesurfer] mri_mask problem
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 +, 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 +, 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 +, 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
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 . 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 +, 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 +, 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 +, 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
>>>&g
Re: [Freesurfer] mri_mask problem
Helo Bruce, I've tryed these options you said and still not working, 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 . 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 +, 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 +, 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 > >>&
Re: [Freesurfer] mri_mask problem
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 . 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 +, 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 +, 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...@hotma
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 . 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 +, 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 +, Gabriel Go.Es. wrote: > > >>>>> > > >&g
Re: [Freesurfer] mri_mask problem
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 . 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 +, 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 doin
Re: [Freesurfer] mri_mask problem
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 . 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 ma
Re: [Freesurfer] mri_mask problem
That works!!! Thank you, Gabriel > Date: Tue, 15 Mar 2011 14:34:00 -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 > > 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 . 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 th
