External Email - Use Caution

HI Bruce,

I have to run recon-all -autorecon1, then substitute the brainmask for my brainmask, changing the brainmask from FS to brainmask.original.FS and labelling my betted image brainmask.mgz and then run recon-all -autorecon2 becuase if I do as you say, FS is generating again its own brainmask and it is being hard. I have been looking as well for a video or something I can have to see how you edit the errors with FS and I have not found anything. Any help with this would be much appreciated.

Yours sincerely, Rosalia

On Thu, Nov 15, 2018 at 7:42 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Rosalia

yes, editing and rerunning recon-all should work. Or update the brainmask.mgz with your own version if you want. We should detect that and retain it.

cheers Bruce

On Wed, 14 Nov 2018, Rosalia Dacosta Aguayo wrote:

...

    External Email - Use Caution

Dear Free Surfer team,

Sorry for double posting but I would like to explain well so it will be easier to understand what I am looking for.

1. I have run recon-all -all in a participant
2. The skull stripped image has skull and dura behind.
3. I can manual edit or I can do -autorecon1 and then supply the

brainmask.nii.gz generated from my betted image. 4. Questions:

a) If I run -autorecon1 and make the substitution of the brainmask: I am afraid this is not going to improve the grey matter and white matter segmentation. So, if this first step is not well solved, I think that

then,

...

no matter if I change my brainmask for a better one, that I will have the same problems with -autorecon2 and -autorecon3, is that correct?

b) If I do manual edition, then I will have to run -autorecon1

again...not

...

sure if this would be the best solution.

As I am new to this, I would greatly appreciate your experience.

Best wishes, Rosalia

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External Email - Use Caution

Hi Bruce,

I will send it you once I am in the lab. In relation to the tutorials, I know that there are tutorials and pdf documentation I have been consulting. But, just to start with editing, it would be helpful to see how another person is doing it in a video or explain it while he/she is doing it. Now I know

Regards, Rosalia

On Thu, Nov 15, 2018 at 9:35 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Rosalia

there are some tutorials on our website. And can you send us the recon-all.log where you have put a new brainmask.mgz into the subject's dir and it gets overwritten? That shouldn't happen

thanks Bruce On Thu, 15 Nov 2018, Rosalia Dacosta Aguayo wrote:

...

    External Email - Use Caution

HI Bruce,

I have to run recon-all -autorecon1, then substitute the brainmask for

my brainmask, changing the

...

brainmask from FS to brainmask.original.FS and labelling my betted image

brainmask.mgz and then run

...

recon-all -autorecon2 becuase if I do as you say, FS is generating again

its own brainmask and it is

...

being hard. I have been looking as well for a video or something I can

have to see how you edit the

...

errors with FS and I have not found anything. Any help with this would

be much appreciated.

...

Yours sincerely, Rosalia

On Thu, Nov 15, 2018 at 7:42 PM Bruce Fischl fischl@nmr.mgh.harvard.edu

wrote:

...

  Hi Rosalia

  yes, editing and rerunning recon-all should work. Or update the
  brainmask.mgz with your own version if you want. We should detect

that and

...

  retain it.

  cheers
  Bruce

    On Wed, 14 Nov 2018,
  Rosalia Dacosta Aguayo wrote:

  >
  >         External Email - Use Caution
  >
  > Dear Free Surfer team,
  >
  > Sorry for double posting but I would like to explain well  so it

will be

...

  > easier to understand what I am looking for.
  >
  > 1. I have run recon-all -all in a participant
  > 2. The skull stripped image has skull and dura behind.
  > 3. I can manual edit or I can do -autorecon1 and then supply the
  > brainmask.nii.gz generated from my betted image.
  > 4. Questions:
  >
  > a) If I run -autorecon1 and make the substitution of the

brainmask: I am

...

  > afraid this is not going to improve the grey matter and white

matter

...

  > segmentation. So, if this first step is not well solved, I think

that then,

...

  > no matter if I change my brainmask for a better one, that I will

have the

...

  > same problems with -autorecon2 and -autorecon3, is that correct?
  >
  > b) If I do manual edition, then I will have to run -autorecon1

again...not

...

  > sure if this would be the best solution.
  >
  > As I am new to this, I would greatly appreciate your experience.
  >
  > Best wishes,
  > Rosalia
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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