Hi - these have different Z voxel dimensions - that probably explains the
difference in FLIRT output as they are really quite different.
Cheers.
On Thu, 7 Oct 2004, bettyann chodkowski wrote:
> hello,
>
> > I didn't realise that you images contain exactly the
> > same data. In that case send us a copy of the header
> > contents (use avwhd) and we can see what the difference
> > is.
>
> the following displays the headers for VolumeA, the volume that
> registers successfully with the standard volume. VolumeA was created
> by an internal philips-to-avw conversion c program:
>
> % avwhd VolumeA.hdr
> filename VolumeA.hdr
>
> sizeof_hdr 348
> data_type
> db_name
> extents 16384
> session_error 0
> regular r
> hkey_un0
> dim0 4
> dim1 128
> dim2 128
> dim3 37
> dim4 99
> dim5 0
> dim6 0
> dim7 0
> vox_units
> cal_units
> unused1 0
> datatype 4
> bitpix 16
> pixdim0 0.0000000000
> pixdim1 1.8999999762
> pixdim2 1.8999999762
> pixdim3 4.0000000000
> pixdim4 2000.0000000000
> pixdim5 0.0000000000
> pixdim6 0.0000000000
> pixdim7 0.0000000000
> vox_offset 0.0000
> funused1 0.0000
> funused2 0.0000
> funused3 0.0000
> cal_max 0.0000
> cal_min 0.0000
> compressed 0
> verified 0
> glmax 1508
> glmin 0
> descrip
> aux_file FM Kirby Research Center
> orient 0
> originator
> origin1 0
> origin2 0
> origin3 0
> generated FM Kirby R
> scannum #-#/g1/lcu
> patient_id XXXXXX,XXX
> exp_date 2004.08.30
> exp_time 14:17:03
> hist_un0
> views 0
> vols_added 0
> start_field 0
> field_skip 0
> omax 0
> omin 0
> smin 0
> smin 0
>
> the following displays the headers for VolumeB, the volume that does
> not register successfully with the standard volume. VolumeB was
> created by an internal matlab conversion program which uses darren
> weber's robust, thorough and easy-to-use mri_toolbox:
>
> % avwhd VolumeB.hdr
> filename VolumeB.hdr
>
> sizeof_hdr 348
> data_type
> db_name
> extents 16384
> session_error 0
> regular r
> hkey_un0
> dim0 4
> dim1 128
> dim2 128
> dim3 37
> dim4 99
> dim5 0
> dim6 0
> dim7 0
> vox_units mm
> cal_units
> unused1 0
> datatype 16
> bitpix 32
> pixdim0 4.0000000000
> pixdim1 1.8999999762
> pixdim2 1.8999999762
> pixdim3 3.0000000000
> pixdim4 1.0000000000
> pixdim5 0.0000000000
> pixdim6 0.0000000000
> pixdim7 0.0000000000
> vox_offset 0.0000
> funused1 1.0000
> funused2 0.0000
> funused3 0.0000
> cal_max 0.0000
> cal_min 0.0000
> compressed 0
> verified 0
> glmax 2576
> glmin 0
> descrip Lit-Visual SENSE|TR=2|FOV=[240 147 240]|scanRez=[80
> 80]|slgap=1
> aux_file
> orient 0
> originator
> origin1 8224
> origin2 8224
> origin3 8224
> generated mri_toolbx
> scannum
> patient_id
> exp_date 10-09-2004
> exp_time 21-16-17.3
> hist_un0
> views 0
> vols_added 0
> start_field 0
> field_skip 0
> omax 0
> omin 0
> smin 0
> smin 0
>
> i changed some fields, one-by-one, in VolumeB to see if that made a
> difference in registration. nope -- not at all. the immediate
> differences are:
>
> vox_units, datatype, bitpix, pixdim0, pixdim3 (this had been
> corrected), pixdim4, funused1 (roi_scale in mri_toolbox), glmax,
> descrip, origin1, origin2, origin3 (mri_toolbox sets originator to
> [spaces] therefore origin1,2,3 are the integer values of
> [space][space]), generated, scannum, patient_id, exp_date, exp_time.
>
> the majority of these fields are ascii descriptor fields. please note
> specifically that header field orient is the same between the two
> volumes -- 0. since FSL does not interpret that field, it does not
> matter anyway.
>
> i am in the process of reading thru graham wideman's incredibly
> informative pages about the analyze format
> (http://www.wideman-one.com/gw/brain/analyze/index.htm). i have not
> yet looked at VolumeA and VolumeB through another display package as a
> double-check with MEDx's "Raw Generic" option.
>
> i send this header info just in case the community sees something
> obvious that i am overlooking.
>
> many thanks to all involved,
> - bettyann
--
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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