Trouble setting environment variables

fuzhenrong commented 6 years ago

hi: i am really confused about how to set the environment variables ,the website list below: HOST=/Users/binarybottle # path on host to access input/output DOCK=/home/jovyan/work # path to HOST from Docker container IMAGE=$DOCK/example_mri_data/T1.nii.gz # input image on HOST ID=arno # ID for brain image my settings is: HOST=/home/fuzhenrong DOCK=/home/fuzhenrong/work IMAGE=$DOCK/example_mri_data/T1.nii.gz ID=arno

fuzhenrong is my hostname,but it run with errors; i really do not know what ID means? because i am a newbie! i am looking forward for your reply ! thank you! good luck! fuzhenrong beihang university

PeerHerholz commented 6 years ago

Hey @fuzhenrong ,

two general things before I address your question:

As can be read on the mindboggle website: Please ask mindboggle related questions on neurostars.org using the tag mindboggle
Please post your error message along with as much information about your settings as possible, so that people here can evaluate your problem and help you more precisely.

Now to your question:

I assume you understood how docker and especially mounting (-v flag) works? As you didn't specify the error, I'm just guessing here: you tried to run the complete mindboggle pipeline and it crashes with an error in the lines of "the input file isn't found"? If that's the case, please check if the example data folder is really where you told your script it is. As you can see within the installation section on the mindboggle website: ID=arno # ID for brain image. So, it's the ID for a specific brain image / participant which will be used as an identifier within all parts of the workflow, e.g. naming respective output folders accordingly. Assuming your ID would be fuzhenrong, the output structure of your mindboggle analysis would look like this:

HTH, best, Peer

binarybottle commented 6 years ago

Thank you @PeerHerholz. @fuzhenrong -- Please don't forget that you must set DOCK=/home/jovyan/work since that's the path to HOST from the Docker container, not from your computer. Also, please follow the examples for setting the paths to the input/output folders on http://mindboggle.readthedocs.io/en/latest/#run-one-command

fuzhenrong commented 6 years ago

thank you very much! it's working!

binarybottle commented 6 years ago

Good to hear! I changed the title of this issue to make it easier for others to find, and am closing the issue now.

fuzhenrong commented 6 years ago

        OK！i will change it soon！

              邮箱：fuzhenrong@buaa.edu.cn

签名由网易邮箱大师定制 On 12/05/2017 22:24, Arno Klein wrote: Good to hear! I changed the title of this issue to make it easier for others to find, and am closing the issue now.

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nipy / mindboggle

Trouble setting environment variables #136