Colin Hansen

Are your input and output directories setup correctly? Going off of your command there should be a directory called inputs and a directory call OUTPUTS in your current working directory....

Can you confirm that you have the files b0.nii.gz, T1.nii.gz, and acqparams.txt in your inputs directory?

Alright, can you provide the entire output log as a txt file?

The current Synb0 output does not include a brain mask. We do run bet to skullstrip the T1 image, but we don't save the mask itself. Anyways you would want...

Hello, It looks like you are missing the path to link the freesurfer license within the docker in your command -v /media/docc/freesurfer-linux-centos6_x86_64-7.1.1/freesurfer/license.txt:/extra/freesurfer/license.txt Let us know if you still see an...

It looks like the epi_reg might have failed, but I can’t be sure without the full output log. Could you provide all of the output text in a txt file?...

For some reason I'm not seeing the attached files. If it is easier, you can email them to me directly [email protected].

Hello Jonatan, I apologize for the late reply. The pipeline can be resource hungry, so usually the best thing to try is to give docker all possible resources. My guess...

Hello Jayashree, It may be possible that the PE of your scan does not match your acqparams.txt file. If this is not the case, could you provide a screenshot of...

Hello Jayashree, The smoothing is intentional. The generation of the synthetic b0 is done at 2.5 iso, and since most DWI acquisition are acquired at higher resolutions, the synthetic b0...