Hello, FSL users;
I am experiencing some confusing behavior when using fsl_motion_outliers.
When I specify a --thresh, the output text file will not be written, and no error message will be displayed:
fsl_motion_outliers -i my_epi.nii -o motion_confound.txt --fd --thresh=0.9
(Result: motion_confound.txt not written, no error messages.)
If I do not specify a --thresh, it works just fine:
fsl_motion_outliers -i my_epi.nii -o motion_confound.txt —fd
(Result: motion_confound.txt is written correctly.)
Confusingly, this is true for some input NIfTI images but not others. When I use data I’ve collected from our scanner (signified by “my_epi.nii” above), the command fails. When I use some data I downloaded from the OpenFMRI project ("openfmri.nii.gz"), the command works:
fsl_motion_outliers -i openfmri.nii.gz -o motion_confound.txt --fd --thresh=0.9
(Result: motion_confound.txt is written correctly.)
I used fslhd to look at the headers of the two files. I don’t know how to evaluate the differences, because I don’t know what would cause fsl_motion_outliers to silently fail. The headers are below.
Any help is appreciated.
Thanks,
Beau Sievers
> fslhd my_epi.nii:
filename my_epi.nii
sizeof_hdr 348
data_type INT16
dim0 4
dim1 80
dim2 80
dim3 35
dim4 88
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.000000
pixdim1 3.000000
pixdim2 3.000000
pixdim3 3.000000
pixdim4 2.000000
pixdim5 0.000000
pixdim6 0.000000
pixdim7 0.000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 0.773382
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 34
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 -3.000000 0.000000 0.000000 122.004005
qto_xyz:2 0.000000 -3.000000 0.000000 133.527054
qto_xyz:3 0.000000 0.000000 3.000000 -26.450888
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Anterior-to-Posterior
qform_zorient Inferior-to-Superior
sform_name Unknown
sform_code 0
sto_xyz:1 0.000000 0.000000 0.000000 0.000000
sto_xyz:2 0.000000 0.000000 0.000000 0.000000
sto_xyz:3 0.000000 0.000000 0.000000 0.000000
sto_xyz:4 0.000000 0.000000 0.000000 0.000000
sform_xorient Unknown
sform_yorient Unknown
sform_zorient Unknown
file_type NIFTI-1+
file_code 1
descrip Philips Medical Systems Achieva 5.1.7
aux_file
> fslhd openfmri.nii.gz:
filename openfmri.nii.gz
sizeof_hdr 348
data_type INT16
dim0 4
dim1 64
dim2 64
dim3 30
dim4 182
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.000000
pixdim1 3.125000
pixdim2 3.125000
pixdim3 5.000000
pixdim4 2.000000
pixdim5 0.000000
pixdim6 0.000000
pixdim7 0.000000
vox_offset 352
cal_max 1652.0000
cal_min 0.0000
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 Scanner Anat
qform_code 1
qto_xyz:1 -3.125000 -0.000000 -0.000000 101.000000
qto_xyz:2 0.000000 3.125000 0.000000 -72.000000
qto_xyz:3 0.000000 0.000000 5.000000 -99.000000
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 Scanner Anat
sform_code 1
sto_xyz:1 -3.125000 0.000000 0.000000 101.000000
sto_xyz:2 0.000000 3.125000 0.000000 -72.000000
sto_xyz:3 0.000000 0.000000 5.000000 -99.000000
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
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