Dear Mark,
Thank you very much for your help!
It worked out well.
Best
Heidi
================================================
Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
[log in to unmask]
www.maastrichtuniversity.nl
www.heidijacobs.nl
Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092
================================================
________________________________________
Van: FSL - FMRIB's Software Library [[log in to unmask]] namens Mark Jenkinson [[log in to unmask]]
Verzonden: donderdag 2 augustus 2012 23:22
Aan: [log in to unmask]
Onderwerp: Re: [FSL] Spatial transform differences in header
Hi,
The differences are all in the origin (308 versus 128 in the first row of the qform/sform).
As long as you are happy that the images make sense to be combined then you can just ignore the warnings and it will still combine the images. If you really want to change the qform/sform information then the easiest way is to use fslcpgeom, which copies the geometry information from the source image to the destination image.
All the best,
Mark
On 2 Aug 2012, at 14:50, Jacobs H (NP) wrote:
> Hi FSL'ers,
>
> I am combining two different data sets and I received an error that the spatial transforms are not the same in the header.
>
> This is the header from a participant from the first dataset:
>
> <nifti_image
> nifti_type = 'NIFTI-1+'
> header_filename = '001_FLAIR_WMHI_to_T1.nii.gz'
> image_filename = '001_FLAIR_WMHI_to_T1.nii.gz'
> image_offset = '352'
> ndim = '3'
> nx = '256'
> ny = '256'
> nz = '256'
> dx = '1'
> dy = '1'
> dz = '1'
> datatype = '2'
> datatype_name = 'UINT8'
> nvox = '16777216'
> nbyper = '1'
> 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 = '-1 0 -0 128 0 0 1 -128 -0 -1 -0 128 0 0 0 1'
> qto_ijk_matrix = '-1 -0 -0 128 -0 -0 -1 128 -0 1 0 128 0 0 0 1'
> quatern_b = '0'
> quatern_c = '0.707107'
> quatern_d = '-0.707107'
> qoffset_x = '128'
> qoffset_y = '-128'
> qoffset_z = '128'
> qfac = '-1'
> qform_i_orientation = 'Right-to-Left'
> qform_j_orientation = 'Superior-to-Inferior'
> qform_k_orientation = 'Posterior-to-Anterior'
> sform_code = '1'
> sform_code_name = 'Scanner Anat'
> sto_xyz_matrix = '-1 0 0 128 0 0 1 -128 0 -1 0 128 0 0 0 1'
> sto_ijk matrix = '-1 0 -0 128 -0 0 -1 128 0 1 0 128 0 0 0 1'
> sform_i_orientation = 'Right-to-Left'
> sform_j_orientation = 'Superior-to-Inferior'
> sform_k_orientation = 'Posterior-to-Anterior'
> num_ext = '0'
>
>
> This is the header of a participant of the second database:
> ifti_image
> nifti_type = 'NIFTI-1+'
> header_filename = '110_FLAIR_WMHI_to_T1.nii.gz'
> image_filename = '110_FLAIR_WMHI_to_T1.nii.gz'
> image_offset = '352'
> ndim = '3'
> nx = '256'
> ny = '256'
> nz = '256'
> dx = '1'
> dy = '1'
> dz = '1'
> datatype = '2'
> datatype_name = 'UINT8'
> nvox = '16777216'
> nbyper = '1'
> 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 = '-1 0 -0 308 0 0 1 -128 -0 -1 -0 128 0 0 0 1'
> qto_ijk_matrix = '-1 -0 -0 308 -0 -0 -1 128 -0 1 0 128 0 0 0 1'
> quatern_b = '0'
> quatern_c = '0.707107'
> quatern_d = '-0.707107'
> qoffset_x = '308'
> qoffset_y = '-128'
> qoffset_z = '128'
> qfac = '-1'
> qform_i_orientation = 'Right-to-Left'
> qform_j_orientation = 'Superior-to-Inferior'
> qform_k_orientation = 'Posterior-to-Anterior'
> sform_code = '1'
> sform_code_name = 'Scanner Anat'
> sto_xyz_matrix = '-1 0 0 308 0 0 1 -128 0 -1 0 128 0 0 0 1'
> sto_ijk matrix = '-1 0 -0 308 -0 0 -1 128 0 1 0 128 0 0 0 1'
> sform_i_orientation = 'Right-to-Left'
> sform_j_orientation = 'Superior-to-Inferior'
> sform_k_orientation = 'Posterior-to-Anterior'
> num_ext = '0'
> />
>
>
> As you can see the matrix dimensions are not the same. How can I transform the matrix dimensions of the second data set to the first one, without changing the orientation?
>
> Thanks!
> Best
> Heidi
> ================================================
> Dr. Heidi Jacobs
> Postdoc researcher
> Faculty of Health, Medicine and Life Sciences
> School for Mental Health and Neurosciences
> Division Cognitive Neuropsychiatry and Clinical Neurosciences
> Alzheimer Center Limburg
> [log in to unmask]
> www.maastrichtuniversity.nl
> www.heidijacobs.nl
>
> Dr. Tanslaan 12, 6229 ET Maastricht
> P.O. Box 616, 6200 MD Maastricht, The Netherlands
> T +31 43 38 84 090 F +31 43 38 84 092
> ================================================
> ________________________________________
>
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