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