[ERROR] invalid first line for key/value file

1

Hi,

I have ran tckedit using the following:

tckedit -include R_T_uncinate.nii.gz -include R_E_uncinate.nii.gz wholebrain_track.tck R_uncinate_test.tck -force -quiet

This command works, but when trying to look at the resulting file in mrview I get the following error:

[ERROR] invalid first line for key/value file “/Volumes/dml/ajbarnett/Halle_DTI/s220/dti_pasternak_mb3_vx2_PA/R_uncinate.tck” (expected “mrtrix tracks”)

mrview is able to open up older .tck files that I made about a month ago, but any new ones created with tckedit do not work. In between this time, I ran brew update && brew upgrade which updated mrtrix.

How can I get tckedit/mrview back to working?

Any help on why this is happening would be greatly appreciated.

Alex

2

That’s unexpected. I don’t think there’s been any significant changes to the track file writing code for some time. Can I ask to run the following and copy/paste the output here?

ls -l R_uncinate.tck
head R_uncinate.tck
tckinfo -debug R_uncinate.tck

Thanks,
Donald

3

Below is the output when I enter those commands:

ls -l R_uncinate.tck 
-rwx------  1 alexbarnett  staff  8940608 Jan 17 12:24 R_uncinate.tck
head R_uncinate.tck 
tckinfo -debug R_uncinate.tck
tckinfo: [DEBUG] No config file found at "/etc/mrtrix.conf"
tckinfo: [DEBUG] No config file found at "/Users/alexbarnett/.mrtrix.conf"
tckinfo: [DEBUG] reading key/value file "R_uncinate.tck"...
tckinfo: [ERROR] invalid first line for key/value file "R_uncinate.tck" (expected "mrtrix tracks")

Thanks,

Alex

4

Does this command really produce no output…? I don’t see how that can happen… Any chance you can share the file with me on some way so I can inspect it more closely?

5

I have messaged you a google drive share link.

6

I’ve had a quick look at your file: it contains 8.6MB of zeros. I have no idea what could cause this. What version of MRtrix3 are you running? What does tckedit -version report? And does tckgen produce usable output? Is its version the same as tckedit (i.e. do you get the same version with tckgen -version)?

7

Below is the version information, but the wholebrain.tck I was using was likely from a previous version of tckgen. I hadn’t thought to re-run tckgen. I just re-ran it now, and then performed tckedit and the resulting file is now functional and fine.

tckedit -version

== tckedit 2b8e7d0c ==
64 bit release version, built Jan 17 2019, using Eigen 3.3.7
Author(s): Robert E. Smith (robert.smith@florey.edu.au)
Copyright (c) 2008-2018 the MRtrix3 contributors.
This Source Code Form is subject to the terms of the Mozilla Public
License, v. 2.0. If a copy of the MPL was not distributed with this
file, you can obtain one at Mozilla Public License, version 2.0
MRtrix3 is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty
of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
For more details, see http://www.mrtrix.org/

tckgen -version

== tckgen 2b8e7d0c ==
64 bit release version, built Jan 17 2019, using Eigen 3.3.7
Author(s): J-Donald Tournier (jdtournier@gmail.com) and Robert E. Smith (robert.smith@florey.edu.au)
Copyright (c) 2008-2018 the MRtrix3 contributors.
This Source Code Form is subject to the terms of the Mozilla Public
License, v. 2.0. If a copy of the MPL was not distributed with this
file, you can obtain one at Mozilla Public License, version 2.0
MRtrix3 is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty
of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
For more details, see http://www.mrtrix.org/

8

That’s really odd… Does this mean the issue is now resolved? I’m not sure we’ll ever figure out what happened with that problematic tckedit run…

9

It is resolved. Thanks for the help. Not sure we will ever discover the root of this. Might have been in the use of a previous version a tckgen with a newer version of tckedit, but we may never know.