Hi Doug, that's correct. I think the problem is perhaps that the original NIFTI file has a very narrow range of values, between 43.7308 and 43.8476, to cover the whole range of tissues in the image. It is an average over several subjects, and before skull stripping, there are hardly any zeros in the image. Is there a way to rescale the file? Thanks, Caspar
2013/12/30 Douglas Greve <gr...@nmr.mgh.harvard.edu> > And macaque_25_model-MNI.nii is the non-binary image? And > macaque_stripped_mask.nii.gz is the binary mask? If so, the command looks > right to me. > doug > > > On 12/30/13 12:08 PM, Caspar M. Schwiedrzik wrote: > > Hi Doug, > this is the command line input: > mri_mask macaque_25_model-MNI.nii macaque_stripped_mask.nii.gz > macaque_stripped_final2.nii > this is the terminal output: > DoAbs = 0 > Found 14652800 voxels in mask > Writing masked volume to macaque_stripped_final2.nii...done. > The same thing happens when I use nii.gz or mgz files. > > Caspar > > > > 2013/12/30 Douglas Greve <gr...@nmr.mgh.harvard.edu> > >> >> what is your command line and terminal output? >> >> >> >> On 12/30/13 10:22 AM, Caspar M. Schwiedrzik wrote: >> >> Hi Freesurfer Experts, >> I am trying to apply a mask that I made with FSL's bet to a NIFTI file >> that I got from someone else. >> The mask looks fine, the NIFTI file is in float format, does not contain >> NaNs or negative values, but the overall values are all pretty low (in the >> 40ies). When I try to apply the mask to the NIFTI file using mri_mask, the >> output I get is essentially a copy of the mask (only zeros and ones). The >> same happens if I use fslmaths. >> Any advice would be very much appreciated. >> Thanks, Caspar >> >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://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 >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
