Thanks Bruce!

However, as you suspected this does not seem to work: mri_extract_label mri/aseg.mgz 24 mri/mask_code24.mgz gives a tiny volume of a couple of hundred voxels in the middle of the brain (part of 3rd ventricle). I assume here that code 24 is the correct code for all CSF in aseg.mgz.

I guess an alternative would be to take the volume of inner skull minus the volume of everything including and below pial surface. How would one go about doing that? Or would you suggest other ways?

Bests,

Tommi

Hi Tommi

you can use mri_extract_label to pull out the labels you want, but the sulcal CSF labels may not be great since the manual labeling that is the basis of the aseg was done on only T1 images.

cheers Bruce

On Wed, 8 Dec 2010 raij@nmr.mgh.harvard.edu wrote:

...

Hi,

We are trying to create a CSF volume mask from structural MEMPRAGE T1 data (we also have ME FLASH 5/30 ->PD if needed). We are interested in two CSF compartments:

• "superficial" CSF outside grey matter and inside inner skull
• "deep" CSF inside ventricles

Is there a way to simply extract these from aseg.mgz or how should we go about this?

Thanks!

-Tommi

---

Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

You can also use mri_binarize with the --match flag. It does the same thing, but you can give it multiple match values. There is also a --ventricles option (excludes 4th ventricle).

doug

Bruce Fischl wrote:

Hi Tommi,

no, you need to also extract the left and right ventricles and the inferior lateral ventricles.

cheers Bruce

On Wed, 8 Dec 2010 raij@nmr.mgh.harvard.edu wrote:

...

Thanks Bruce!

However, as you suspected this does not seem to work: mri_extract_label mri/aseg.mgz 24 mri/mask_code24.mgz gives a tiny volume of a couple of hundred voxels in the middle of the brain (part of 3rd ventricle). I assume here that code 24 is the correct code for all CSF in aseg.mgz.

I guess an alternative would be to take the volume of inner skull minus the volume of everything including and below pial surface. How would one go about doing that? Or would you suggest other ways?

Bests,

Tommi

...

Hi Tommi

you can use mri_extract_label to pull out the labels you want, but the sulcal CSF labels may not be great since the manual labeling that is the basis of the aseg was done on only T1 images.

cheers Bruce

On Wed, 8 Dec 2010 raij@nmr.mgh.harvard.edu wrote:

...

Hi,

We are trying to create a CSF volume mask from structural MEMPRAGE T1 data (we also have ME FLASH 5/30 ->PD if needed). We are interested in two CSF compartments:

• "superficial" CSF outside grey matter and inside inner skull
• "deep" CSF inside ventricles

Is there a way to simply extract these from aseg.mgz or how should we go about this?

Thanks!

-Tommi

---

Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. _______________________________________________ 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