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

Yendiki, Anastasia Fri, 13 Jan 2017 07:12:39 -0800

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

On Thu, Jan 12, 2017 at 9:06 PM, Derek A Pisner <dpisner@utexas.edu> wrote:

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

--
Derek Pisner

Derek Pisner