did you try using freeview? For example:

freeview -v brain.mgz

On Fri, 31 Aug 2012, Borzello, Mia wrote:

Hi,

I make it an mgz. When trying to load (tried using a load and read command) to make sure it looks okay, but it's not working. How can I view this mgz file or ascertain that it has an error?

Thanks, m ________________________________________ From: Louis Nicholas Vinke [vinke@nmr.mgh.harvard.edu] Sent: Friday, August 31, 2012 10:29 AM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull

Hi, You need to add an extension onto the file name, something like brain.mgz or brain.nii. The extension will tell it what format to save the output in. -Louis

On Fri, 31 Aug 2012, Borzello, Mia wrote:

...

Hi freesurfer family,

I am trying to create the inner skull boundary and ran: mri_watershed -atlas - surf -useSRAS mri.nii brain

However, after it finished running it said it was saving "brain", but "brain" was an unknown file type. Am i supposed to specify that somewhere?

Thanks in advance, m

---

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

Also, is there a way to create a skull from a CT scan? ________________________________________ From: Borzello, Mia Sent: Friday, August 31, 2012 12:17 PM To: freesurfer Subject: RE: [Freesurfer] creating a skull

I've been referred to the following link on the freesurfer site to handle this, but is this still current (i.e. is linux still needed to do this?): http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html

thanks, m ________________________________________ From: Louis Nicholas Vinke [vinke@nmr.mgh.harvard.edu] Sent: Friday, August 31, 2012 10:29 AM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull

Hi, You need to add an extension onto the file name, something like brain.mgz or brain.nii. The extension will tell it what format to save the output in. -Louis

On Fri, 31 Aug 2012, Borzello, Mia wrote:

Hi freesurfer family,

I am trying to create the inner skull boundary and ran: mri_watershed -atlas - surf -useSRAS mri.nii brain

However, after it finished running it said it was saving "brain", but "brain" was an unknown file type. Am i supposed to specify that somewhere?

Thanks in advance, m

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi Mia

what platform are you running on?

Bruce On Fri, 31 Aug 2012, Borzello, Mia wrote:

I've been referred to the following link on the freesurfer site to handle this, but is this still current (i.e. is linux still needed to do this?): http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html

thanks, m ________________________________________ From: Louis Nicholas Vinke [vinke@nmr.mgh.harvard.edu] Sent: Friday, August 31, 2012 10:29 AM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull

Hi, You need to add an extension onto the file name, something like brain.mgz or brain.nii. The extension will tell it what format to save the output in. -Louis

On Fri, 31 Aug 2012, Borzello, Mia wrote:

...

Hi freesurfer family,

I am trying to create the inner skull boundary and ran: mri_watershed -atlas - surf -useSRAS mri.nii brain

However, after it finished running it said it was saving "brain", but "brain" was an unknown file type. Am i supposed to specify that somewhere?

Thanks in advance, m

---

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

no, that should be fine On Tue, 4 Sep 2012, Borzello, Mia wrote:

I'm using Unix. Should I try something else?

Thanks, m ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 03, 2012 2:45 PM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull

Hi Mia

what platform are you running on?

Bruce On Fri, 31 Aug 2012, Borzello, Mia wrote:

...

I've been referred to the following link on the freesurfer site to handle this, but is this still current (i.e. is linux still needed to do this?): http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html

thanks, m ________________________________________ From: Louis Nicholas Vinke [vinke@nmr.mgh.harvard.edu] Sent: Friday, August 31, 2012 10:29 AM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull

Hi, You need to add an extension onto the file name, something like brain.mgz or brain.nii. The extension will tell it what format to save the output in. -Louis

On Fri, 31 Aug 2012, Borzello, Mia wrote:

...

Hi freesurfer family,

I am trying to create the inner skull boundary and ran: mri_watershed -atlas - surf -useSRAS mri.nii brain

However, after it finished running it said it was saving "brain", but "brain" was an unknown file type. Am i supposed to specify that somewhere?

Thanks in advance, m

---

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