Question about error log and pipeline

[ajdneuro]

I ran the pipeline on some of my data and got an error. Does the pipeline look for a specific orientation of the data.

I was wondering if I could have some help with what the issue is (attached).

Also a more broad questions, what is the upper limit in age for the pipeline? Would infants 1-2 not be appropriate? Thanks!

subject1-session1.segmentation.log

[jcupitt]

Hello again @ajdneuro ,

The pipeline has moved here:

https://github.com/BioMedIA/dhcp-structural-pipeline

Could you open your issue there, please?

[MartinBa9210]

Hello @jcupitt, I've got a similar problem.

Running the docker like:

$ docker run --rm -t
-u $(id -u):$(id -g)
-v $PWD/anat:/data
biomedia/dhcp-structural-pipeline:latest subject1 session1 28
-T1 anat/sub-CC00099AN18_ses-34200_T1w.nii.gz -T2 anat/sub-CC00099AN18_ses-34200_T2w.nii.gz -t 2

gives me errors in the log file
subject1-session1.segmentation.log

How can i fix that?

Thank you for your help.

Best,
Martin

[ajdneuro]

Hi @jcupitt
I can't seem to find the tab to open the new issue on the dhcp-structural-pipeline page?

Thanks,
Alex

[jcupitt]

You're right, I'd forgotten to turn issues on, sorry about that.

https://github.com/BioMedIA/dhcp-structural-pipeline/issues/new

I wondered why all our users were so happy, duh. Thanks for pointing this out.