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 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Yendiki%2C+Anastasia%22> Fri, 13 Jan 2017 07:12:39 -0800 <https://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 <dpis...@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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