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 ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Derek A Pisner [dpis...@utexas.edu] Sent: Thursday, January 12, 2017 10:06 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error 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
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