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Hi Rolf, if you upload the image at http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi and send me the upload ID I'll have a look cheers christian On 23 Jul 2007, at 19:16, Rolf Heckemann wrote: > 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 ____ 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