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DevelopingHCP / structural-pipeline

dHCP structural pipeline
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Question about error log and pipeline #6

Open ajdneuro opened 6 years ago

ajdneuro commented 6 years ago

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 commented 6 years ago

Hello again @ajdneuro ,

The pipeline has moved here:

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

Could you open your issue there, please?

MartinBa9210 commented 6 years ago

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 commented 5 years ago

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

Thanks, Alex

jcupitt commented 5 years ago

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.