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
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