Dear Kristina,
The problem seems to be that your system is more sensitive to the lack
of single quotes in the dt = 3.0 line than other systems. You can fix this
by replacing the line
/home/software/fsl/bin/fslhd -x filtered_func_data | sed 's/ dt = .*/ dt = '3.0'/g' > tmpHeader
with
/home/software/fsl/bin/fslhd -x filtered_func_data | sed "s/ dt = .*/ dt = \'3.0\'/g" > tmpHeader
and checking that the fslcreatehd line then works.
If this does work then you can fix your version of FEAT to do the right thing by changing the line
fsl:exec "${FSLDIR}/bin/fslhd -x filtered_func_data | sed 's/ dt = .*/ dt = '$fmri(tr)'/g' > tmpHeader"
to
fsl:exec "${FSLDIR}/bin/fslhd -x filtered_func_data | sed 's/ dt = .*/ dt = @$fmri(tr)@/g' | tr @ \' > tmpHeader"
which I hope will work with your machine.
All the best,
Mark
On 6 Jun 2012, at 22:26, Kristina Skatun wrote:
> Dear Mark,
>
> Thank you for you input! These are the contents of the tmpHeader:
>
> <nifti_image
> nifti_type = 'NIFTI-1+'
> header_filename = 'filtered_func_data.nii.gz'
> image_filename = 'filtered_func_data.nii.gz'
> image_offset = '352'
> ndim = '4'
> nx = '64'
> ny = '64'
> nz = '5'
> nt = '45'
> dx = '4'
> dy = '4'
> dz = '6'
> dt = 3.0
> datatype = '16'
> datatype_name = 'FLOAT32'
> nvox = '921600'
> nbyper = '4'
> byteorder = 'LSB_FIRST'
> scl_slope = '1'
> scl_inter = '0'
> xyz_units = '2'
> xyz_units_name = 'mm'
> time_units = '8'
> time_units_name = 's'
> descrip = 'FSL4.1'
> qform_code = '1'
> qform_code_name = 'Scanner Anat'
> qto_xyz_matrix = '-4 0 -0 0 0 4 -0 0 0 0 6 0 0 0 0 1'
> qto_ijk_matrix = '-0.25 0 -0 -0 0 0.25 0 -0 -0 -0 0.166667 -0 0 0 0 1'
> quatern_b = '0'
> quatern_c = '1'
> quatern_d = '0'
> qoffset_x = '0'
> qoffset_y = '0'
> qoffset_z = '0'
> qfac = '-1'
> qform_i_orientation = 'Right-to-Left'
> qform_j_orientation = 'Posterior-to-Anterior'
> qform_k_orientation = 'Inferior-to-Superior'
> sform_code = '1'
> sform_code_name = 'Scanner Anat'
> sto_xyz_matrix = '-4 0 0 0 0 4 0 0 0 0 6 0 0 0 0 1'
> sto_ijk matrix = '-0.25 -0 -0 -0 -0 0.25 -0 -0 -0 -0 0.166667 -0 0 0 0 1'
> sform_i_orientation = 'Right-to-Left'
> sform_j_orientation = 'Posterior-to-Anterior'
> sform_k_orientation = 'Inferior-to-Superior'
> num_ext = '0'
> />
>
>
> Regards,
>
> Kristina
>
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