Re: [Freesurfer] Recon-all after edits

[Bruce Fischl]

Hi Manuel

yes, that is true. The control points might make the wm edits unnecessary
cheers
Bruce
On 
Fri, 31 Mar 2017, Manuel Delgado wrote:

> 
> Thank you Bruce. However, doing the recon-all for both the wm and the cp
> will have the same result as adding the control points and recon-all in a
> first step, and then doing the wm edits and recon-all again? I think that if
> you perform the wm edits in the result of having added the cp, the edits you
> need may be different than if you have not done the cp step previously. Is
> this right? Thus, even though it is possible to do an only recon-all step
> for both edits, is it recommendable to do it?
> 
> On 30/03/17 15:51, Bruce Fischl wrote:
> 
> Hi Manuel
> 
> -autorecon2-cp runs all the steps that autorecon2-wm does so it is 
> redundant. If you run autorecon2-cp and autorecon3 you will get everything 
> (unless you edit the aseg)
> 
> cheers
> Bruce
> On Thu, 30 Mar 2017, Manuel Delgado wrote:
> 
> Dear list,
> There is an issue that I have been concerned about since the beginning of my
> FS learning, as I have found somehow contradictory information in the
> tutorials. Is there a way to do an only recon-all after all the edits have
> been made to a subject? For example, if you have edited all the possible
> steps (skullstrip, control points, wm and pial surface) is it possible to
> use all the flags for each step in one only step? Something like:
> recon-all -autorecon2-cp -autorecon2-wm -autorecon-pial -autorecon3 -subjid
> 
> 
> Or on the other hand each step needs its own recon-all with its appropriate
> flag?
> Thank you
> 
> --
> Manuel Delgado Alvarado, MD
> Neurology Department
> Neuroimaging Unit
> Valdecilla Biomedical Research Institute, IDIVAL
> Santander, SPAIN
> 
> 
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> l
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> erly
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Re: [Freesurfer] Recon-all after edits

[Manuel Delgado]

Thank you Bruce. However, doing the recon-all for both the wm and the cp
will have the same result as adding the control points and recon-all in a
first step, and then doing the wm edits and recon-all again? I think that
if you perform the wm edits in the result of having added the cp, the edits
you need may be different than if you have not done the cp step previously.
Is this right? Thus, even though it is possible to do an only recon-all
step for both edits, is it recommendable to do it?
On 30/03/17 15:51, Bruce Fischl wrote:

Hi Manuel

-autorecon2-cp runs all the steps that autorecon2-wm does so it is
redundant. If you run autorecon2-cp and autorecon3 you will get everything
(unless you edit the aseg)

cheers
Bruce
On Thu, 30 Mar 2017, Manuel Delgado wrote:


Dear list,
There is an issue that I have been concerned about since the beginning of my
FS learning, as I have found somehow contradictory information in the
tutorials. Is there a way to do an only recon-all after all the edits have
been made to a subject? For example, if you have edited all the possible
steps (skullstrip, control points, wm and pial surface) is it possible to
use all the flags for each step in one only step? Something like:
recon-all -autorecon2-cp -autorecon2-wm -autorecon-pial -autorecon3 -subjid


Or on the other hand each step needs its own recon-all with its appropriate
flag?
Thank you

--
Manuel Delgado Alvarado, MD
Neurology Department
Neuroimaging Unit
Valdecilla Biomedical Research Institute, IDIVAL
Santander, SPAIN



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Re: [Freesurfer] Recon-all after edits

[Octavian Lie]

Hello Bruce,

I think this ties to one of my previous questions. Most of the volumes I
processed need both wm and pial edits (typically deleting incorrectly added
voxels for both). More recently, I was editing wm.mgz for wm and
brainmask.mgz for pial. From the wiki, if changes are made for both wm/pia,
one can run recon-all -autorecon2 -autorecon3 and both changes would be
incorporated, however with some volumes this does not happen: pial edits
are incorporated correctly, but wm edits are not, I am not sure why, event
though FS6.0.0 sees edits (running recon-all with -showedits points to
edits in sm.mgz as well, and those edits propagate into filled.mgz. So
next, I plan editing brain.finalsurfs.manedit.mgz for pia ( it turns out
one cannot edit this also for wm when that means deleting voxels for wm),
wm.mgz for wm, then run -autorecon2-wm -autorecon3. Is this a strategy, and
if there are alternatives, please let me know. Also, for some reason,
running recon with '-make all'  does not seem to work.

Thank you,

Octavian


On Thu, Mar 30, 2017 at 8:51 AM, Bruce Fischl 
wrote:

> Hi Manuel
>
> -autorecon2-cp runs all the steps that autorecon2-wm does so it is
> redundant. If you run autorecon2-cp and autorecon3 you will get everything
> (unless you edit the aseg)
>
> cheers
> Bruce
> On Thu, 30 Mar 2017, Manuel Delgado wrote:
>
> > Dear list,
> > There is an issue that I have been concerned about since the beginning
> of my
> > FS learning, as I have found somehow contradictory information in the
> > tutorials. Is there a way to do an only recon-all after all the edits
> have
> > been made to a subject? For example, if you have edited all the possible
> > steps (skullstrip, control points, wm and pial surface) is it possible to
> > use all the flags for each step in one only step? Something like:
> > recon-all -autorecon2-cp -autorecon2-wm -autorecon-pial -autorecon3
> -subjid
> > 
> >
> > Or on the other hand each step needs its own recon-all with its
> appropriate
> > flag?
> > Thank you
> >
> > --
> > Manuel Delgado Alvarado, MD
> > Neurology Department
> > Neuroimaging Unit
> > Valdecilla Biomedical Research Institute, IDIVAL
> > Santander, SPAIN
> >
> >
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>
>
> 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
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] Recon-all after edits

[Bruce Fischl]

Hi Manuel

-autorecon2-cp runs all the steps that autorecon2-wm does so it is 
redundant. If you run autorecon2-cp and autorecon3 you will get everything 
(unless you edit the aseg)

cheers
Bruce
On Thu, 30 Mar 2017, Manuel Delgado wrote:

> Dear list,
> There is an issue that I have been concerned about since the beginning of my
> FS learning, as I have found somehow contradictory information in the
> tutorials. Is there a way to do an only recon-all after all the edits have
> been made to a subject? For example, if you have edited all the possible
> steps (skullstrip, control points, wm and pial surface) is it possible to
> use all the flags for each step in one only step? Something like:
> recon-all -autorecon2-cp -autorecon2-wm -autorecon-pial -autorecon3 -subjid
> 
> 
> Or on the other hand each step needs its own recon-all with its appropriate
> flag?
> Thank you
> 
> --
> Manuel Delgado Alvarado, MD
> Neurology Department
> Neuroimaging Unit
> Valdecilla Biomedical Research Institute, IDIVAL
> Santander, SPAIN
> 
>
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[Freesurfer] Recon-all after edits

[Manuel Delgado]

Dear list,
There is an issue that I have been concerned about since the beginning of
my FS learning, as I have found somehow contradictory information in the
tutorials. Is there a way to do an only recon-all after all the edits have
been made to a subject? For example, if you have edited all the possible
steps (skullstrip, control points, wm and pial surface) is it possible to
use all the flags for each step in one only step? Something like:
recon-all -autorecon2-cp -autorecon2-wm -autorecon-pial -autorecon3 -subjid


Or on the other hand each step needs its own recon-all with its appropriate
flag?
Thank you

-- 
*Manuel Delgado Alvarado, MD*
Neurology Department
Neuroimaging Unit
Valdecilla Biomedical Research Institute, IDIVAL
Santander, SPAIN
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contains patient information, please contact the Partners Compliance HelpLine at
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