Mindboggle's new website and Docker app

neuroimaging
mindboggle

#1

The Mindboggle project has an updated website (http://mindboggle.info) with new documentation, including Docker installation instructions (thanks, @akeshavan!). Please take a look and give it a try! I would really appreciate as much feedback as possible before its upcoming launch. An article is under review documenting and evaluating Mindboggle’s open source software for extracting features and labels and analyzing their shapes. All data and documentation are available from a new Open Science Framework project page (https://osf.io/ydyxu/).

Cheers,
@rno


#2

now on bioarxiv: http://biorxiv.org/content/early/2016/12/03/091322


#3

how to set the environment var for mindboggle, the website is said it is tricky! the instruction is not in details.


#4

and on PLoS Computational Biology: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005350


#5

If you are using the Docker container, the environment variables are listed: http://mindboggle.readthedocs.io/en/latest/#installation


#6

ok thank you! i will try


#7

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


#8

Please set the following for the Docker container:
DOCK=/home/jovyan/work


#9

Thank you! I have set the environment as
HOST=/home/fuzhenrong
DOCK=/home/jovyan/work
IMAGE=$DOCK/example_mri_data/T1.nii.gz
ID=arno
but when i trying to run the command on the website
docker run --rm -ti -v $HOST:$DOCK nipy/mindboggle $IMAGE --id $ID
it get errors.
traits.trait_errors.TraitError: The trait ‘T1_files’ of a ReconAllInputSpec instance is an existing file name, but the path ‘/home/jovyan/work/example_mri_data/T1.nii.gz’ does not exist.
in fact, the path is exist! why? thang you very much for your reply!
fuzhenrong
beihang university


#10

This has grown into an issue – Could you please post the above as a mindboggle github issue?:
https://github.com/nipy/mindboggle/issues and let’s take it from there!

Thanks!