FSLUtils

FIRST > BET > FSLView > FSLUtils

FSL provides a set of simple applications to explore, analyze and operate images. Here, some of them.

FSLInfo	Displaying information about the image

fsl5.0-fslinfo intro/structural.nii.gz

data_type      INT16
dim1           256
dim2           256
dim3           128
dim4           1
datatype       4
pixdim1        1.0000000000
pixdim2        1.0000000000
pixdim3        1.2500000000
pixdim4        1.0000000000
cal_max        25500.0000
cal_min        20.0000
file_type      NIFTI-1+

FSLHd	Displaying high description about the image

fsl5.0-fslhd intro/structural.nii.gz

filename intro/structural.nii.gz sizeof_hdr 348 data_type INT16 dim0 3 dim1 256 dim2 256 dim3 128 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units s datatype 4 nbyper 2 bitpix 16 pixdim0 0.0000000000 pixdim1 1.0000000000 pixdim2 1.0000000000 pixdim3 1.2500000000 pixdim4 1.0000000000 pixdim5 0.0000000000 pixdim6 0.0000000000 pixdim7 0.0000000000 vox_offset 352 cal_max 25500.0000 cal_min 20.0000 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 -1.000000 0.000000 -0.000000 0.000000 qto_xyz:2 0.000000 1.000000 -0.000000 0.000000 qto_xyz:3 0.000000 0.000000 1.250000 0.000000 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 -1.000000 0.000000 0.000000 0.000000 sto_xyz:2 0.000000 1.000000 0.000000 0.000000 sto_xyz:3 0.000000 0.000000 1.250000 0.000000 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 FSL4.1 aux_file

FSLStats	Compute some statistics from image intensities, as minimum, maximum, etc...

fsl5.0-fslstats intro/highres.nii.gz -R -r

 0.000000 32767.000000 0.000000 16711.169922 

Here the first two values corresponds to minimum and maximum values (-R option), the other two values are the minimum and maximum if the outer tails of the intensity distribution are ignored.

fsl5.0-fslstats intro/highres.nii.gz -l 1 -R -r

 11.000000 32767.000000 2696.991943 18976.724609 

Here the -l 1 option indicate the lower limit (avoiding zero values)

fsl5.0-fslstats intro/highres.nii.gz -l 1 -R -r -m -M

 11.000000 32767.000000 2696.991943 18976.724609 12057.230531 12057.230531

Here -m and -M indicates the mean and mean without zeros respectively and correspond to fifth and sixth values.