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: > > 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: jlcan...@upo.es > http://www.upo.es/neuroaging/es/ > > > > ----- Mensaje original ----- > > De: Bruce Fischl <fis...@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: jlcan...@upo.es > > > http://www.upo.es/neuroaging/es/ > > > > > > ----- Mensaje original ----- > > > De: Bruce Fischl <fis...@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: jlcan...@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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
