Hi Jared,

Mechanically, yes - you would use the edit voxels tool and then use the right button to remove the voxels you do not want.

I'm not sure I understand exactly what you are trying to do - and if you eventually want to use Freesurfer to obtain surfaces etc, this will not work. I'd suggest saving your brainmask as something else, and edit that - this way you still have a viable brainmask.mgz to obtain results with.

Jenni

On Mon, 11 Jun 2007, Jared Conley wrote:

Hi Jenni,

I am trying to edit the greyscale images of the brainmask.mgz. We are trying to generate an ICC map with only grey/white matter and we need to exclude a few structures that are not removed in the skull-stripping step (i.e. some of the cranial nerves, pituitary, etc.). I assume that I begin by using the "Edit Voxels tool (a)", but I do not know where to go from there.

Thanks,

Jared

Jenni Pacheco wrote:

...

Hi Jared,

What happens when you try and edit? What type of editing are you trying to do? Do you have the right tools selected? I'm going to need a little bit more information on what you are doing and what is going wrong. Thanks,

Jenni

On Mon, 11 Jun 2007, Jared Conley wrote:

...

FreeSurfer community,

I am attempting to manually edit brainmask.mgz in TkMedit and cannot figured out how to do so based on the info in the Wiki. I load the file in X11 with the command <tkmedit subjid brainmask.mgz> and see the images just fine, but I cannot seem to manually edit them like I can in the segmentation file. Any ideas?

Thanks,

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

Jenni,

Another question for you. What is the consequence of running autorecon2 after editing on the brainmask.mgz file itself. You mentioned something about it not working if we want to obtain surfaces--what did you mean exactly? CSF surfaces?

Ideally, we are editing the brainmask.mgz file so that autorecon2 only segments the brain according to our protocol (which eliminates pituitary, cranial nerves). In the end, we only need segmentation results of basal ganglia and the grey/white matter/lat. ventricles. If we could get the intracranial volume measurements that would be ideal, but I don't think this is possible.

Thanks,

Jared

Jenni Pacheco wrote:

Hi Jared,

Mechanically, yes - you would use the edit voxels tool and then use the right button to remove the voxels you do not want.

I'm not sure I understand exactly what you are trying to do - and if you eventually want to use Freesurfer to obtain surfaces etc, this will not work. I'd suggest saving your brainmask as something else, and edit that - this way you still have a viable brainmask.mgz to obtain results with.

Jenni

On Mon, 11 Jun 2007, Jared Conley wrote:

...

Hi Jenni,

I am trying to edit the greyscale images of the brainmask.mgz. We are trying to generate an ICC map with only grey/white matter and we need to exclude a few structures that are not removed in the skull-stripping step (i.e. some of the cranial nerves, pituitary, etc.). I assume that I begin by using the "Edit Voxels tool (a)", but I do not know where to go from there.

Thanks,

Jared

Jenni Pacheco wrote:

...

Hi Jared,

What happens when you try and edit? What type of editing are you trying to do? Do you have the right tools selected? I'm going to need a little bit more information on what you are doing and what is going wrong. Thanks,

Jenni

On Mon, 11 Jun 2007, Jared Conley wrote:

...

FreeSurfer community,

I am attempting to manually edit brainmask.mgz in TkMedit and cannot figured out how to do so based on the info in the Wiki. I load the file in X11 with the command <tkmedit subjid brainmask.mgz> and see the images just fine, but I cannot seem to manually edit them like I can in the segmentation file. Any ideas?

Thanks,

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

Hi Jenni,

Sorry for the confusion. We are more familiar with our own registration/segmentation system, where we edit before segmentation not after. Anyway, thank you for the advice. We will edit the aseg.mgz file instead.

Thanks again,

Jared

Jenni Pacheco wrote:

Hi Jared,

It's still not completely clear to me what you are trying to do. By segmentation values do you just mean the volumes that will come out of the aseg.mgz? If thats what you mean you should make these edits to the aseg.mgz itself.

I'm not certain what will happen if you make these edits to the brainmask - but I'd guess the surfaces won't be accurate, some things may not run at all.

Jenni

On Mon, 11 Jun 2007, Jared Conley wrote:

...

Jenni,

Another question for you. What is the consequence of running autorecon2 after editing on the brainmask.mgz file itself. You mentioned something about it not working if we want to obtain surfaces--what did you mean exactly? CSF surfaces? Ideally, we are editing the brainmask.mgz file so that autorecon2 only segments the brain according to our protocol (which eliminates pituitary, cranial nerves). In the end, we only need segmentation results of basal ganglia and the grey/white matter/lat. ventricles. If we could get the intracranial volume measurements that would be ideal, but I don't think this is possible.

Thanks,

Jared

Jenni Pacheco wrote:

...

Hi Jared,

Mechanically, yes - you would use the edit voxels tool and then use the right button to remove the voxels you do not want.

I'm not sure I understand exactly what you are trying to do - and if you eventually want to use Freesurfer to obtain surfaces etc, this will not work. I'd suggest saving your brainmask as something else, and edit that - this way you still have a viable brainmask.mgz to obtain results with.

Jenni

On Mon, 11 Jun 2007, Jared Conley wrote:

...

Hi Jenni,

I am trying to edit the greyscale images of the brainmask.mgz. We are trying to generate an ICC map with only grey/white matter and we need to exclude a few structures that are not removed in the skull-stripping step (i.e. some of the cranial nerves, pituitary, etc.). I assume that I begin by using the "Edit Voxels tool (a)", but I do not know where to go from there.

Thanks,

Jared

Jenni Pacheco wrote:

...

Hi Jared,

What happens when you try and edit? What type of editing are you trying to do? Do you have the right tools selected? I'm going to need a little bit more information on what you are doing and what is going wrong. Thanks,

Jenni

On Mon, 11 Jun 2007, Jared Conley wrote:

...

FreeSurfer community,

I am attempting to manually edit brainmask.mgz in TkMedit and cannot figured out how to do so based on the info in the Wiki. I load the file in X11 with the command <tkmedit subjid brainmask.mgz> and see the images just fine, but I cannot seem to manually edit them like I can in the segmentation file. Any ideas?

Thanks,

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

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