Hi,
That seems very strange.
Can you upload the data to:
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and send us the reference number.
We can hopefully then sort it out.
All the best,
Mark
On 24 Nov 2010, at 11:20, Najmeh Khalili Mahani wrote:
> Hello list
>
> I am attaching a picture of a strange shift I see after averaging a
> 4D-file across time, using "fslmaths -Tmean".
>
> In green, you see one volume of the 4D input file. It is registered to
> MNI152. All other volumes in the 4D file are also well aligned.
> However, when averaging this well-aligned-4D file, I get the shifted
> image (in red and blue).
>
> The only difference in orientation-related parameters is in slice
> slope: it is 1 for the input-4D (the green one) but 0 for the
> output-3D (the red/blue) . (see the complete header files below.)
>
> I am using fsl 4.1.4 (on linux).
>
> Many thanks for any hacks, hints, suggestions!
>
> Naj
>
>
> filename 4D_Z_000_merged.nii.gz
>
> sizeof_hdr 348
> data_type FLOAT32
> dim0 4
> dim1 91
> dim2 109
> dim3 91
> dim4 21
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 16
> nbyper 4
> bitpix 32
> pixdim0 0.0000000000
> pixdim1 2.0000000000
> pixdim2 2.0000000000
> pixdim3 2.0000000000
> pixdim4 1.0000000000
> pixdim5 0.0000000000
> pixdim6 0.0000000000
> pixdim7 0.0000000000
> vox_offset 352
> cal_max 25986.5781
> 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 37
> 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 MNI_152
> qform_code 4
> qto_xyz:1 -2.000000 0.000000 -0.000000 90.000000
> qto_xyz:2 0.000000 2.000000 -0.000000 -126.000000
> qto_xyz:3 0.000000 0.000000 2.000000 -72.000000
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Right-to-Left
> qform_yorient Posterior-to-Anterior
> qform_zorient Inferior-to-Superior
> sform_name MNI_152
> sform_code 4
> sto_xyz:1 -2.000000 0.000000 0.000000 90.000000
> sto_xyz:2 0.000000 2.000000 0.000000 -126.000000
> sto_xyz:3 0.000000 0.000000 2.000000 -72.000000
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Right-to-Left
> sform_yorient Posterior-to-Anterior
> sform_zorient Inferior-to-Superior
> file_type NIFTI-1+
> file_code 1
> descrip FSL4.0
> aux_file
>
>
> filename average_Z_000_merged_ak.nii.gz
> sizeof_hdr 348
> data_type FLOAT32
> dim0 3
> dim1 91
> dim2 109
> dim3 91
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 16
> nbyper 4
> bitpix 32
> pixdim0 0.0000000000
> pixdim1 2.0000000000
> pixdim2 2.0000000000
> pixdim3 2.0000000000
> pixdim4 1.0000000000
> pixdim5 0.0000000000
> pixdim6 0.0000000000
> pixdim7 0.0000000000
> vox_offset 352
> cal_max 5.2499
> cal_min -15047905050731643669264520726869704704.0000
> scl_slope 0.000000
> 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 MNI_152
> qform_code 4
> qto_xyz:1 -2.000000 0.000000 -0.000000 90.000000
> qto_xyz:2 0.000000 2.000000 -0.000000 -126.000000
> qto_xyz:3 0.000000 0.000000 2.000000 -72.000000
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Right-to-Left
> qform_yorient Posterior-to-Anterior
> qform_zorient Inferior-to-Superior
> sform_name MNI_152
> sform_code 4
> sto_xyz:1 -2.000000 0.000000 0.000000 90.000000
> sto_xyz:2 0.000000 2.000000 0.000000 -126.000000
> sto_xyz:3 0.000000 0.000000 2.000000 -72.000000
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Right-to-Left
> sform_yorient Posterior-to-Anterior
> sform_zorient Inferior-to-Superior
> file_type NIFTI-1+
> file_code 1
> descrip FSL4.0
> aux_file
> <fslmaths_meants_error.tiff>
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