Hi Johannes, as the mri_convert help says, you should not use this to make images appear "correctly" in fslview. If your volume starts off with the correct geometry (which it probably has), then you will make it incorrect by changing the orientation string. FSL has tools to accomplish what you are trying to do (a combination of fslswapdim and another program).

doug

Dear all, I have acquired 4D data on a Siemens machine, and I'm using mri_convert to turn the DICOMs into NIFTI files. Now, I would like to "rectify" the 4D NIFTI volume, such that the principal axes display in a standard way in fslview. I can do this for 3D files like this is, and it works a charm for all sorts of original orientations: mri_convert --out_orientation LAS input.nii rectified_output.nii

However, when I'm using a 4D NIFTi file as input, only the first volume is included in the rectified output and the rest is truncated. I was wondering if this is a known limitation, and if there is another tool I could use on 4D files which would save me having to split them up before reorientation? BTW, I've tried this on Freesurfer 4.3.0 and 4.0.5. Thanks in advance for your help, Johannes _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer