Hi Derek - It looks like it fails, but I suspect that it may be something unrelated to the warning. Can you please upload a zip file with this subject's TRACULA directories (dmri, dmri.bedpostX, dlabel, dpath, scripts) for me here:
https://gate.nmr.mgh.harvard.edu/filedrop2/
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 2:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error
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
On Sun, Jan 15, 2017 at 1:27 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Derek A Pisner [dpisner@utexas.edumailto:dpisner@utexas.edu] Sent: Sunday, January 15, 2017 11:47 AM To: freesurfer@nmr.mgh.harvard.edumailto: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
Yendiki, Anastasiahttps://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Yendiki%2C+Anastasia%22 Fri, 13 Jan 2017 07:12:39 -0800https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20170113
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.edumailto: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
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-- Derek Pisner