glad it worked out :) On Wed, 20 Jul 2011, r.nava...@itab.unich.it wrote:
> 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
