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
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