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FSL  July 2007

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Subject:

Re: BET and NIFTI

From:

Rolf Heckemann <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 23 Jul 2007 19:16:44 +0100

Content-Type:

text/plain

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text/plain (160 lines)

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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