Dear FS team, I'm working on some NIFTI images which I want to convert to mgz. When I try to do this, I get:
mri_convert /home/avdleij1/ID1000/ID1000_scans/CON_ID1000/NIFTI/sc0219-20101101-0003-T13DTFESENSE.nii.gz /home/avdleij1/ID1000/ID1000_scans/CON_ID1000/FREESURFER/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/avdleij1/ID1000/ID1000_scans/CON_ID1000/NIFTI/sc0219-20101101-0003-T13DTFESENSE.nii.gz... WARNING: MRIsetRas2VoxFromMatrix(): voxels sizes are inconsistent (1,1) (1,1) (1,1.6) This is probably due to shear in the vox2ras matrix Input Vox2RAS ------ 0.013 0.018 1.600 -125.223; -1.000 -0.001 0.020 158.408; -0.002 1.000 -0.029 -85.678; 0.000 0.000 0.000 0.000; TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.012721, -0.999918, -0.00162597) j_ras = (0.0180632, -0.00139604, 0.999836) k_ras = (0.999756, 0.0127483, -0.0180439) writing to /home/avdleij1/ID1000/ID1000_scans/CON_ID1000/FREESURFER/mri/orig/001.mgz... I'm not sure what's going on here, but I assume that something isn't right in the matrix, as my data (Phillips par/rec converted to NIFTI) are 1*1*1 mm (see below). I assume that our local conversion app does something fishy with the matrix. I'm completely in the dark on how to solve this. Any ideas would be greatly appreciated! Best, Andries avdleij1@debian:~/ID1000/ID1000_scans/CON_ID1000/NIFTI$ fslhd sc0219-20101101-0003-T13DTFESENSE.nii.gz filename sc0219-20101101-0003-T13DTFESENSE.nii.gz sizeof_hdr 348 data_type FLOAT32 dim0 3 dim1 256 dim2 256 dim3 160 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units s datatype 16 nbyper 4 bitpix 32 pixdim0 0.0000000000 pixdim1 1.0000000000 pixdim2 1.0000000000 pixdim3 1.0000000000 pixdim4 1.0000000000 pixdim5 0.0000000000 pixdim6 0.0000000000 pixdim7 0.0000000000 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 0.012721 0.018063 0.999756 -125.222908 qto_xyz:2 -0.999918 -0.001396 0.012748 158.408218 qto_xyz:3 -0.001626 0.999836 -0.018044 -85.677658 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 Aligned Anat sform_code 2 sto_xyz:1 0.012721 0.018063 1.599609 -125.222908 sto_xyz:2 -0.999918 -0.001396 0.020397 158.408218 sto_xyz:3 -0.001626 0.999836 -0.028870 -85.677658 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Anterior-to-Posterior sform_yorient Inferior-to-Superior sform_zorient Left-to-Right file_type NIFTI-1+ file_code 1 descrip FSL4.1 aux_file
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