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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
