Missing Scale_L4

[peterN908]

Hi there :)

When I run the ./pipeline_test.sh on the branch 'origin/spm-bspline' with N_shm = 6 I receive the following error:

file xxx/dMRIharmonization/lib/tests/connectom_prisma/template/Scale_L4.nii.gz does not exist .

Would you have any tips in debugging this?

FYI; if i re-run the pipeline_test.sh with N_shm = 2 I do not get this issue

[peterN908]

Is it that the number of gradient directions on the test data is insufficient to support N_shm > 2?

[tashrifbillah]

Hi @peterN908 ,

Is it that the number of gradient directions on the test data is insufficient

Yes.

I included a table in our documentation describing the numbers. Tests are for quick checking only, so I released a data with only 13 diffusion-weighted gradients, which forces N_shm to be 2.

When I run the ./pipeline_test.sh on the branch 'origin/spm-bspline' with N_shm = 6

Curious, how do you do that? I do not provide a way to set up N_shm manually as part of ./pipeline_test.sh.

[peterN908]

Thanks for your help I hard coded in the n_shm because the config file could not be found (similar issue to https://github.com/pnlbwh/dMRIharmonization/issues/65)

[tashrifbillah]

the config file could not be found

That I can try to solve. So you tried ./pipeline_test.sh as it is and it complained about the inexistence?

[peterN908]

Yes exactly

I checked the /TMP/ folder and the config files being created certainly do exist

[tashrifbillah]

Thanks for reporting, I shall try to reproduce at my end.

[tashrifbillah]

With ./pipeline_test.sh, the issue could not be reproduced. Regardless, feel free to switch to the master branch. That employs tempfile.gettempdir method to write the configuration to a tempfile.