Hello,
I have some data where the TR in the NIFTI header is specified in ms instead of seconds. I've confirmed this with fslhd. When I load the data into FEAT, it gets mistakenly listed as a TR of 2000 seconds.
In the past, I've worked around this by just running the raw data through fslmaths first. For example, running fslmaths raw_data.nii float_data.nii -odt float seems to fix the issue and feat then recognizes the TR correctly. While fslmaths in FSL 5.0.11 produces output that fixes this issue, in FSL 6.0.1, the output of fslmaths leaves 2000 in the pixdim4 entry of the header, but changes the time_units entry to be seconds.
Is there something I can do to read my data into FEAT in FSL 6.0.1 correctly other than manually changing the NIFTI headers myself with fsledithd? I've pasted below the nifti header of one of my raw data files.
Thank you in advance for your help!
Best,
Anthony Sali
sizeof_hdr 348
data_type INT16
dim0 4
dim1 64
dim2 64
dim3 40
dim4 278
dim5 1
dim6 1
dim7 1
vox_units mm
time_units ms
datatype 4
nbyper 2
bitpix 16
pixdim0 0.000000
pixdim1 3.000000
pixdim2 3.000000
pixdim3 3.000000
pixdim4 2000.000000
pixdim5 1.000000
pixdim6 1.000000
pixdim7 1.000000
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 -2.996200 0.140011 0.056392 94.193001
qto_xyz:2 -0.135177 -2.987675 0.235642 125.543571
qto_xyz:3 0.067157 0.232803 2.990200 -58.944221
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 Scanner Anat
sform_code 1
sto_xyz:1 -2.996202 0.140008 0.056392 94.193001
sto_xyz:2 -0.135174 -2.987676 0.235641 125.543571
sto_xyz:3 0.067157 0.232804 2.990200 -58.944221
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Anterior-to-Posterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip
aux_file
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