Hi Anastasia,
See attached log. Hard to tell, but it does seem that trac-all fails after this warning.
Thanks for taking a look!
Derek Pisner
Doctoral Student
CLA 4.600
Mood Disorders Laboratory (MDL)
Department of Psychology | The University of Texas at Austin
Hi Derek - It sounds like the programs that you used to convert from dicom to nifti and to resample from anisotropic nifti to isotropic nifti don't copy the TE and TR info in the header correctly. This information is not needed to run -paths, however. Does trac-all stop running after this warning, or does it keep going? Can you attach your entire trac-all.log file? Thanks!
a.y
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu ] on behalf of Derek A Pisner [dpisner@utexas.edu]
Sent: Sunday, January 15, 2017 11:47 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error
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.yOn Thu, Jan 12, 2017 at 9:06 PM, Derek A Pisner <dpisner@utexas.edu> wrote:
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/A
pplications/freesurfer/bin/tra c-all -no-isrunning -path -c /work/04171/dpisner/data/ABM/T RACULA/tractography_output/s00 2/trac_config.txt niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
WARNING: niiRead(): unknown time units 0 in /work/04171/dpisner/data/ABM/T
RACULA/tractography_output/s00 2/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
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