Skip to content

Commit

Permalink
Merge pull request #703 from rbroc/master
Browse files Browse the repository at this point in the history
small fixes to docs
  • Loading branch information
adelavega committed Dec 13, 2019
2 parents 8207a4d + da6b009 commit 697f71a
Show file tree
Hide file tree
Showing 2 changed files with 7 additions and 8 deletions.
13 changes: 6 additions & 7 deletions docs/cli/usage.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,25 +3,24 @@
This assumes that you are using the Docker Container.
Docker commands for _neuroscout-cli_ will always being with:

docker run -it
docker run -it --rm

Assuming you've already created an analysis on neuroscout.org, and have its analysis id (e.g.: `5xH93`), you can run it in one line:

docker run -it neuroscout/neuroscout-cli run /outdir 5xH93
docker run -it --rm neuroscout/neuroscout-cli run /out 5xH93

Neuroscout will download the necessary images, analysis bundle, and fit your model.

## Mounting Volumes

Most likely, you'll want to mount at least two volumes , in order to cache input data (`/data`), and inspect output results (`/out`)
Most likely, you'll want to mount at least two volumes, in order to cache input data (`/work`), and inspect output results (`/out`).

In this example, we mount both of these directories to local volumes:

docker run -it -v /local/datadir:/data -v /local/outdir:/out neuroscout/neuroscout-cli run /out 5xH937f

The necessary dataset will be downloaded to your local volume (`/local/datadir`), and next time you run a model with the same dataset, it will not need to re-download the fMRI data.
The model-fitting outputs will also be locally saved at `/local/outdir`.
docker run -it --rm -v /local/datadir:/work -v /local/outdir:/out neuroscout/neuroscout-cli run /out 5xH937f

In this command, the path preceding `:/work` specifies the directory where the data will be stored (i.e. your local volume `/local/datadir`). The next time you run a model with the same dataset, it will not need to re-download the fMRI data. The path preceding `:/out` specifies the directory where the model-fitting outputs will be saved (`/local/outdir`). </br>
Note that you need to specify **absolute paths** for both directories.

## Command-Line Arguments

Expand Down
2 changes: 1 addition & 1 deletion neuroscout/config/datasets/ds001545.json
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"LearningTemporalStructure": {
"preproc_address": "https://github.com/neuroscout-datasets/LearningTemporalStructure.git",
"path": "/datasets/raw/ds001545/",
"summary": "Passiving watching of three clips from the movie 'The Grand Budapest Hotel', six times each",
"summary": "Passive watching of three clips from the movie 'The Grand Budapest Hotel', six times each",
"url": "https://openneuro.org/datasets/ds001545",
"tasks": {
"movie": {
Expand Down

0 comments on commit 697f71a

Please sign in to comment.