Hi Anastasia,
I am getting the following error when running trac-all –paths on all of my diffusion images using the newly updated TRACULA:
*vlogin03.ls5(97)$* /work/04171/dpisner/stampede/Applications/freesurfer/bin/trac-all -no-isrunning -path -c /work/04171/dpisner/data/ABM/TRACULA/tractography_output/s002/trac_config.txt
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
WARNING: niiRead(): unknown time units 0 in /work/04171/dpisner/data/ABM/TRACULA/tractography_output/s002/dmri/dwi.nii.gz
Any idea what’s going on here?
Thanks as always,
Derek Pisner
Doctoral Student
CLA 4.600
Mood Disorders Laboratory (MDL)
Department of Psychology | The University of Texas at Austin
P.S. Here is the header information on my dwi.nii.gz file:
*vlogin03.ls5(105)$* fslhd dwi.nii.gz
filename dwi.nii.gz
sizeof_hdr 348
data_type FLOAT32
dim0 4
dim1 115
dim2 115
dim3 56
dim4 55
dim5 1
dim6 1
dim7 1
vox_units Unknown
time_units Unknown
datatype 16
nbyper 4
bitpix 32
pixdim0 0.000000
pixdim1 2.000000
pixdim2 2.000000
pixdim3 2.000000
pixdim4 1.000000
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 Unknown
qform_code 0
qto_xyz:1 2.000000 0.000000 0.000000 0.000000
qto_xyz:2 0.000000 2.000000 0.000000 0.000000
qto_xyz:3 0.000000 0.000000 2.000000 0.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Aligned Anat
sform_code 2
sto_xyz:1 -2.000000 0.000000 0.000000 114.551003
sto_xyz:2 0.000000 2.000000 0.000000 -74.456001
sto_xyz:3 0.000000 0.000000 2.000000 -0.960182
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
aux_file