is rawavg.mgz the image on the left? if not, and you want the image on the left to be the skull-stripped image, then use that instead of rawavg.mgz.
you can use tkregister2 to create a transform aligning your image to a colin27 image, then use mri_vol2vol to reslice the image.
nick
On Tue, 2009-10-13 at 14:03 +0200, Jose Luis Cantero Lorente wrote:
Hi there,
we used mri_mask to obtain skull stripped images keeping the resolution of original images, but don't understand why the voxel intensity changes between both images (please find attached the image comparison with the Freesurfer commands used). I have two questions regarding this process:
- Is it possible to obtain skull stripped images by using mri_mask
keeping the identical resolution and voxel intensity as in the original MRI (left column in the attached file)?
- Is it possible to convert this skull-stripped images into .nii
transformed to colin27 coordinates from Freesurfer?
Thanks in advance.
Best, Jose
Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla
- Spain -
Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor@upo.es http://www.upo.es/neuroaging/es/
----- Mensaje original -----
De: Bruce Fischl fischl@nmr.mgh.harvard.edu
Fecha: Viernes, Octubre 9, 2009 7:53 pm
Asunto: Re: [Freesurfer] skull stripped image with the original resolution
yes, you could use mri_mask. The problem is once you went down to 8 bits you've lost that resolution and resampling to 16 won't recover it, it will just fill it out with zeros On Fri, 9 Oct 2009, Jose Luis Cantero Lorente wrote:
Thanks, Bruce.
Is it possible to do that from Freesurfer? How?
What I really need is to convert into .nii the Freesurfer skull
stripped image with 16-32 bit resolution and transformed colin27 coordinates (MNI single subject template). Is that possible using the skull stripped image provided by Freesurfer?
Best, Jose
Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla
- Spain -
Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor@upo.es http://www.upo.es/neuroaging/es/
----- Mensaje original ----- De: Bruce Fischl fischl@nmr.mgh.harvard.edu Fecha: Viernes, Octubre 9, 2009 7:43 pm Asunto: Re: [Freesurfer] skull stripped image with the original
resolution>
you'll then need to use that to mask the input volume to recover the true original 16 (or 12) bit resolution.
On Fri, 9 Oct 2009, Nick Schmansky wrote:
add -odt int to the mri_convert flag:
mri_convert -odt int brainmask.mgz brainmask.nii
which saves the output file in 'integer' data format.
On Fri, 2009-10-09 at 18:16 +0200, Jose Luis Cantero Lorente
wrote:>>>> Hi there,
would it be feasible to save to .nii the skull stripped image
obtained with Freesurfer but keeping the original image resolution? As it is, Freesurfer allows you this operation, but the resultant .nii image comes with a poor resolution (8-bits) which is useless for my purpose.
Thanks in advance.
Best, Jose
Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla
- Spain -
Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor@upo.es http://www.upo.es/neuroaging/es/
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Jose Luis Cantero Lorente -
Nick Schmansky