Hi Riccardo, I don't understand what 4) is. A couple of points:
1. if you give mri_convert .nii.gz as an output extension it will do the gzipping for you. 2. If you give mri_convert the flag -rl <template volume> it will reslice the input volume "like" the template. not sure if that solves your problem. Can you describe in more detail what you are trying to accomplish? cheers, Bruce On Tue, 19 Jul 2011, r.nava...@itab.unich.it wrote: > Hi FS expert. > I need to port my T1 and a couple of ROIs from mgz to nii.gz. The same > for many subjects. The issue's about dimensions. When I use fslview, > it respond me that "All overlays must have same dimensions as the base > image!". Indeed T1's 256x256x256 with voxel sizee 1mm3, ROIs are > differents dimensions and 0.5mm3 voxel size. > To work now I use this pipeline: > > ( command line :) ) > 1) mri_convert ---> nii > 2) gzip ---> nii.gz > 3) fslmaths t1 -sub t1 t1_zero > 4) mricron t1_zero -l 0 -h 100 -o roi1.nii.gz > ( GUI only :( ) > 5) (from mricron) save as nifti roi1_ok.nii.gz > > Is there a way to do (5) from command line? > > Thanx > > Riccardo > > > _______________________________________________ > 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 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.
