Hi Anastasia,
Thanks for the quick response!
The TE and the TR are both listed as 0.00 with mri_info. Of note, these dwi images have been resampled from anisotropic to isotropic voxels using an in-house python script. I noticed that this error comes up only for the resampled, but not the original image. I am guessing this is the underlying source of the problem and has less to do with trac-all. What does trac-all need from the header to successfully run -paths? How can the header be corrected in freesurfer so that it will run successfully? Strangely, the TE also comes up as being equal to 0 in the original, anisotropic, image... The TR is what appears to be different and perhaps that is the source of the niiRead() warning? See below.
Many Thanks,
Derek
vlogin03.ls5(69)$ mri_info dwi.nii.gz
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
Volume information for dwi.nii.gz
type: nii
dimensions: 115 x 115 x 56 x 55
voxel sizes: 2.000000, 2.000000, 2.000000
type: FLOAT (3)
fov: 230.000
dof: 0
xstart: -115.0, xend: 115.0
ystart: -115.0, yend: 115.0
zstart: -56.0, zend: 56.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
nframes: 55
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -0.4490
: x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 40.5440
: x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 55.0398
Orientation : LAS
Primary Slice Direction: axial
voxel to ras transform:
-2.0000 0.0000 0.0000 114.5510
0.0000 2.0000 0.0000 -74.4560
0.0000 0.0000 2.0000 -0.9602
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -8
ras to voxel transform:
-0.5000 -0.0000 -0.0000 57.2755
-0.0000 0.5000 -0.0000 37.2280
-0.0000 -0.0000 0.5000 0.4801
-0.0000 -0.0000 -0.0000 1.0000
vlogin03.ls5(84)$ mri_info aniso_eddy_corrected_data_denoised.nii.gz
Volume information for eddy_corrected_data_denoised.nii.gz
type: nii
dimensions: 256 x 256 x 37 x 55
voxel sizes: 0.898400, 0.898400, 3.000002
type: FLOAT (3)
fov: 229.990
dof: 0
xstart: -115.0, xend: 115.0
ystart: -115.0, yend: 115.0
zstart: -55.5, zend: 55.5
TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
Hi Derek - Thanks for testing the 6.0 release candidate. Does it keep running after this message? Since this is a warning and not an error, it may not be critical. If you run mri_info on your dwi.nii.gz, does the TE show up as zero?
Best, a.y
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
--
Derek Pisner