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:
1. 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)?
2. 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
> >>>
> >>>
> >>>
> >>
> >
> >
> >
>