Hi Bruce, (4) open in mricon t1_zero and use roi1 as overlay...anyway -rl option is what I was looking for! :D Thank you.... New pipiline is:
(command line:) (a) mri_convert t1.mgz t1.nii.gz (b) for roiX -> mri_convert roiX.mgz roiX.nii.gz -rl t1.mgz (it works with t1.nii.gz also ) Thank you so much! Riccardo Quoting Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > 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. > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
