Hi Doug, thanks for your input. I turns out that there is some problem when converting minc to NIFTI with float. I got a hold of the original minc file and converted it to NIFTI with minc2nii using integer, and now the values are in a reasonable range and the skull stripping works. Thanks! Caspar
2013/12/30 Douglas Greve <gr...@nmr.mgh.harvard.edu> > > That should not be a problem. Certainly it should not cause everything to > go to 1s and 0s. What version of FS are you using? And you say the same > thing happens with FSL? Try using mri_convert to convert the nonbinary > image to another nifti file and see if you get 1s and 0s. If not, then try > that file as input. You can also try fscalc, something like > > fscalc input.nii mul mask.nii -o output.nii > > should accomplish the same thing > > doug > > > > > > On 12/30/13 1:12 PM, Caspar M. Schwiedrzik wrote: > > 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. >>> >>> >> >> > >
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