Running ComputeGlyphMaps under Linux: error message 'Aborted'

Submitted by timschaefer on

Since I was unable to get ComputeGlyphMaps to work under MacOS, I tried under Linux. I installed v3.1.3 for Linux on an Ubuntu 16.04 LTS server and once more followed the manual up to the part where ComputeGlyphMaps is run. Then I run ComputeGlyphMaps:

$ ComputeGlyphMaps subject1dti_proc/subject1dti_L0_DT.nii

The image file (subject1dti_proc/subject1dti_L0_DT_2_36.png) does NOT exist after the command finishes, and the Aborted message sounds like something went wrong. But what? The file I gave it (subject1dti_L0_DT.nii) is one of the 2 output files of the EstimateTensorWLLS command (see manual).


I also tried running ComputeGlyphMaps against the raw nifti file instead (which gives the same error message), and also against the subject1dti_proc/subject1dti_L0_AM.nii file (which results in a segfault). What am I doing wrong?


Submitted by irfanogl on Fri, 03/01/2019 - 12:16


Hello Tim,

I have never seen ComputeGlyphMaps crash in this way. This is a little weird.

ComputeGlyphMaps is a special executable among all TORTOISE executables.  It is the ONLY executable that is not statically linked so it relies on system libraries, specifically OpenGL libraries from the video card driver.

The way you run it is correct:

ComputeGlyphMaps subject1dti_proc/subject1dti_L0_DT.nii  axial

ComputeGlyphMaps subject1dti_proc/subject1dti_L0_DT.nii  coronal

is the right way to run (with the diffusion tensor DT files), not the other two.

However my suspicion is that there is either somethingunexpected in the DT file or an issue with the OpenGL drivers.

Can you try it with a couple of more datasets? For example the DT file in the AFNI_bootcamp dataset on the Download section and let us know if it happens with all datasets or just one?










Submitted by timschaefer on Mon, 03/04/2019 - 04:26


I gave it a try on the example data and the error stays the same. I hope this is what you wanted me to try:


     [user@linux:~] $ cd data/TORTOISE_V3.1.1_AFNI_bootcamp_DATA_031218/demo_DATA/2b--step2b_initialQC

     [user@linux:~/data/TORTOISE_V3.1.1_AFNI_bootcamp_DATA_031218/demo_DATA/2b--step2b_initialQC] $ ComputeGlyphMaps dti_n_ap_DR_L0_DT.nii coronal
     [user@linux:~/data/TORTOISE_V3.1.1_AFNI_bootcamp_DATA_031218/demo_DATA/2b--step2b_initialQC] $ ComputeGlyphMaps dti_n_ap_DR_L0_DT.nii axial

If this is related to OpenGL libs, what libraries do I need? I am running this on a linux server in some datacenter that does not have a display and no dedicated gfx card, so missing openGL libs could very well be the root of the problem.

Submitted by irfanogl on Mon, 03/04/2019 - 10:43


Hello again,

Okay that looks like the problem then.

Basically, the OpenGL drivers are installed by installing the video card driver. If there is no video card, there is no driver.

and the fact that it happened even with the sample data (which runs fine everywhere else) kind of confirms this.

Just as a side note, the intention behind "ComputeGlyphMaps" is that you run it once as the initial step for your study to make sure that your gradients are correct. While batch processing your data afterwards,  you do not need to run it every single time.   The QC folder in each dataset (if AFNI is installed) will give you the summary information for each dataset.

So my suggestion is to try it in a local computer once to make sure the gradients are fine. Afterwards, you do not need to run it again.