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
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
External Email - Use Caution
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 CautionTo 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
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:
External Email - Use Caution
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
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:
External Email - Use CautionThank 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 CautionTo 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
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:
External Email - Use Caution
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
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:
External Email - Use Caution
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
that will do a bit more than just the skullstripping On Wed, 16 Oct 2019, Krieger, Donald N. wrote:
External Email - Use CautionPlease 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:
External Email - Use Caution
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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 CautionPlease 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 CautionHi 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:
External Email - Use CautionThank 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 CautionTo 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Marianna
I think you can just run recon-all -s <subject> -skullstrip and it will run it for you as it normally does
cheers Bruce On Wed, 16 Oct 2019, Inglese, Marianna wrote:
External Email - Use Caution
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:
External Email - Use Caution
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Bruce,
shall I do that with my original T1 as input or the T1.mgz?
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 17:58 A: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Oggetto: Re: [Freesurfer] R: R: R: recon-all skull stripping
Hi Marianna
I think you can just run recon-all -s <subject> -skullstrip and it will run it for you as it normally does
cheers Bruce On Wed, 16 Oct 2019, Inglese, Marianna wrote:
External Email - Use CautionDear 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 CautionPlease 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 CautionHi 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:
External Email - Use CautionThank 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 CautionTo 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
it will figure out the input and output for you On Wed, 16 Oct 2019, Inglese, Marianna wrote:
External Email - Use Caution
Hi Bruce,
shall I do that with my original T1 as input or the T1.mgz?
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 17:58 A: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Oggetto: Re: [Freesurfer] R: R: R: recon-all skull stripping Hi Marianna
I think you can just run recon-all -s <subject> -skullstrip and it will run it for you as it normally does
cheers Bruce On Wed, 16 Oct 2019, Inglese, Marianna wrote:
External Email - Use Caution
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:
External Email - Use Caution
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Inglese, Marianna -
Krieger, Donald N.