If you mean save the screenshot to an image without the background ( the background is transparent), you can do so with the free GIMP. The tool is in one of the menus and it's called "Select by Color", click the black portion and cut it.

Save it to an image format which understands transparency ( PNG or TIFF )

Krish

On Apr 9, 2009, at 6:05 PM, Douglas N Greve wrote:

what do you mean to save it without the background? Those voxels have to have some value.

slew@nmr.mgh.harvard.edu wrote:

...

Hi,

I want to remove the background 0 in the segmented volume like aseg.mgz, and saved the volume without the background. What is the simplest way to do it?

Best, Seok

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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

All voxels in the segmentation still have to have a value. Do you want to change the segmentation voxel values in the background to something? If you want to change them to 0, then use mri_mask.

doug

slew@nmr.mgh.harvard.edu wrote:

Hi,

My previous question seems misleading. Here is what I want to do.

I have a labeled volume by mri_watershed, which classifies 6 tissue types and an exterior (i.e. background). I want to have a labeled volume without the exterior.

Thanks, Seok

...

If you mean save the screenshot to an image without the background ( the background is transparent), you can do so with the free GIMP. The tool is in one of the menus and it's called "Select by Color", click the black portion and cut it.

Save it to an image format which understands transparency ( PNG or TIFF )

Krish

On Apr 9, 2009, at 6:05 PM, Douglas N Greve wrote:

...

what do you mean to save it without the background? Those voxels have to have some value.

slew@nmr.mgh.harvard.edu wrote:

...

Hi,

I want to remove the background 0 in the segmented volume like aseg.mgz, and saved the volume without the background. What is the simplest way to do it?

Best, Seok

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

---

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