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Dear all,

from this:

(...) Removes the skull from mri/T1.mgz and stores the result in mri/brainmask.auto.mgz and mri/brainmask.mgz. Runs the mri_watershed program. If the strip fails, users can specify seed points (-wsseed) or change the threshold (-wsthresh, -wsmore, -wsless). The -autorecon1 stage ends here.

i guess the function I need is mri_watershed. Now the question is: does recon-all add optional flagged arguments to this function while running recon-all? and which of them?

Thank you.

BW
Marianna
Da: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> per conto di Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Inviato: mercoledì 16 ottobre 2019 17:52
A: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Oggetto: Re: [Freesurfer] R: R: recon-all skull stripping
 
that will do a bit more than just the skullstripping
On Wed, 16 Oct 2019,
Krieger, Donald N. wrote:

>        External Email - Use Caution
>
> Please pardon me for jumping in here.
> I looks like recon-all -autorecon1 will do it, yes?
>
> Best - Don
>
> -----Original Message-----
> From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
> Sent: Wednesday, October 16, 2019 12:48 PM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] R: R: recon-all skull stripping
>
> oh, sure, you can just run that part of recon-all. You don't need to rerun the whole thing cheers Bruce On Wed, 16 Oct 2019, Inglese, Marianna wrote:
>
>>
>>         External Email - Use Caution
>>
>> Hi Bruce,
>>
>> what I mean is that, two of the main outputs of recon-all are T1.mgz
>> (which has the skull) and brain.mgz (which has been skull stripped).
>> For a group of patients, I lost the brain.mgz file and I still have
>> the T1.mgz. I was wondering if there was a way, given T1.mgz as input,
>> to get brain.mgz (avoiding the whole segmentation procedure again).
>>
>> Thank you
>>
>> BW
>> Marianna
>>
>> ______________________________________________________________________
>> ______
>> Da: freesurfer-bounces@nmr.mgh.harvard.edu
>> <freesurfer-bounces@nmr.mgh.harvard.edu> per conto di Bruce Fischl
>> <fischl@nmr.mgh.harvard.edu>
>> Inviato: mercoledì 16 ottobre 2019 17:40
>> A: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Oggetto: Re: [Freesurfer] R: recon-all skull stripping Hi Marianna
>>
>> I'm not sure what you mean by "replicate". The procedure should be the
>> same for all inputs unless you change something explicitly
>>
>> cheers
>> Bruce
>>
>> On Wed, 16 Oct 2019,
>> Inglese, Marianna wrote:
>>
>>>
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>>>
>>> Thank you Bruce.
>>> I thought it was something similar to the FSL bet function, which
>>> extracts the brain using a fractional intensity threshold (0.5 for example).
>>> So I guess I won't be able to replicate the same exact skull
>>> stripping of freesurfer's recon-all.
>>>
>>> BW
>>> Marianna
>>>
>>> _____________________________________________________________________
>>> ______
>> _
>>> Da: freesurfer-bounces@nmr.mgh.harvard.edu
>>> <freesurfer-bounces@nmr.mgh.harvard.edu> per conto di Bruce Fischl
>>> <fischl@nmr.mgh.harvard.edu>
>>> Inviato: mercoledì 16 ottobre 2019 17:23
>>> A: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>> Oggetto: Re: [Freesurfer] recon-all skull stripping Hi Marianna
>>>
>>> the skull stripping is a hybrid procedure that uses both a watershed
>>> algorithm and a deformable surface. There is no single intensity
>>> threshold in it. Maybe I'm misunderstanding your question? There are
>>> parameters you can change (for example the preflooding height), but
>>> there is no intensity thresholding
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Wed, 16 Oct 2019, Inglese, Marianna
>>> wrote:
>>>
>>>>
>>>>         External Email - Use Caution
>>>>
>>>> To whom it may concern,
>>>>
>>>> I am using recon-all to segment many T1s. As I can see, one of the
>>> automatic
>>>> step performed by recon-all is the skull stripping. Would it be
>>>> possible
>>> to
>>>> know the threshold used for the stripping? I guess it is the same
>>> threshold
>>>> everytime. I would like to apply the skull stripping only on other
>>>> T1s
>> and
>>>> need to get the same result.
>>>>
>>>> Thank you very much for the help.
>>>>
>>>> Yours faithfully,
>>>>
>>>> Marianna Inglese
>>>>
>>>> Research fellow, Imperial College London Department of Surgery and
>>>> Cancer
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
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