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Hi Christian Thanks for your reply. On Mon, Jul 23, 2007 at 05:47:44PM +0100, Christian Beckmann wrote: > Hi Rolf, > > what happens when you run avwsize and avwhd on this data set? One $ avwsize file.nii.gz dim1 256 dim2 256 dim3 150 dim4 1 pixdim1 0.9375000000 pixdim2 0.9375000000 pixdim3 1.1999992132 pixdim4 1.0000000000 $ avwhd file.nii.gz filename file.nii.gz sizeof_hdr 348 data_type INT16 dim0 3 dim1 256 dim2 256 dim3 150 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units s datatype 4 nbyper 2 bitpix 16 pixdim0 0.0000000000 pixdim1 0.9375000000 pixdim2 0.9375000000 pixdim3 1.1999992132 pixdim4 1.0000000000 pixdim5 1.0000000000 pixdim6 1.0000000000 pixdim7 1.0000000000 vox_offset 352 cal_max 0.0000 cal_min 0.0000 scl_slope 1.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Scanner Anat qform_code 1 qto_xyz:1 -0.006603 -0.091952 1.194183 -75.056931 qto_xyz:2 -0.928923 0.126385 0.007528 117.192993 qto_xyz:3 0.126350 0.924380 0.117761 -136.721985 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Anterior-to-Posterior qform_yorient Inferior-to-Superior qform_zorient Left-to-Right sform_name Unknown sform_code 0 sto_xyz:1 0.000000 0.000000 0.000000 0.000000 sto_xyz:2 0.000000 0.000000 0.000000 0.000000 sto_xyz:3 0.000000 0.000000 0.000000 0.000000 sto_xyz:4 0.000000 0.000000 0.000000 0.000000 sform_xorient Unknown sform_yorient Unknown sform_zorient Unknown file_type NIFTI-1+ file_code 1 descrip aux_file > possibility is to use the -c option to make sure that bet starts off > inside the brain - this is useful if your data has a lot of neck > included in the image, by default, BET is initialised at the COG > which - if there's a lot of neck - is too low. Another possibility is The data set doesn't contain more neck than others where I've used bet successfully. I've played with the -c parameter, but can't work out what reference the x, y and z parameters are in -- the millimetre coordinates in fslview don't seem to match. > to use the -f and -g options, see command line help for more info This is what I've been trying, and this is where it fails. Let me rephrase the problem: the "vertical" gradient that I parameterize with the -g option is not vertical -- it goes from ear to ear in this image. I can manipulate the axes to force it to fit, but this is obviously not safe, since I will then get inconsistent orientations when I load the file into fslview or other software that reads the NIFTI header properly. Please see http://www.soundray.org/betproblem.png for a screenshot that illustrates the issue. Regards Rolf > cheers > Christian > > > On 23 Jul 2007, at 17:10, Rolf Heckemann wrote: > > >I am getting strange results using bet on a NIFTI file -- it seems to > >use a wrong interpretation of the orientation. For testing, I ran > >"bet file.nii.gz file-bet.nii.gz -g 1": I get an outline that cuts > >into the brain on the right, but leaves the left untouched (expected > >result is a large brain outline at the bottom, small at the top). > >FSLView loads the input file correctly (i.e. S, I, A, P, R and L > >labels are as expected). I tried working around the issue by running > >betpremask on file.nii, but although it generates a reasonably-looking > >premasked image, the same orientation problem occurs when I use bet on > >it. > > > >How can I get bet to read this type of file properly? > > > >Thanks > > > >Rolf > > > > > >-- > >Rolf A Heckemann, PhD > >Research Associate > >Division of Neuroscience and Mental Health > >MRC Clinical Sciences Centre > >Imperial College London > >Hammersmith Hospital Campus > >Du Cane Road > >London W12 0HS > >United Kingdom > > ____ > Christian F. Beckmann > University Research Lecturer > Oxford University Centre for Functional MRI of the Brain (FMRIB) > John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK. > [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann > tel: +44 1865 222551 fax: +44 1865 222717