CSS Python HTML JavaScript
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
css
doc
examples
img
js
nidmviewer
.gitignore
CHANGELOG.md
CONTRIBUTORS.md
LICENSE
README.md
index.html
requirements.txt
setup.py

README.md

nidm-viewer

NIDM Results Viewer

  • parses peak coordinates and associated brain maps
  • interactive coordinate browsing
  • save image to file (export)
  • produces html code for embedding, or local viewer
  • uses font brain for nidm and brain imaging icons

Documentation

Complete documentation is available

Installation

To install

pip install nidmviewer

To install development version:

pip install git+git://github.com/vsoch/nidmviewer.git

Running Examples

Command Line

When installing with setup.py, an executable, nidmviewer is installed in your bin to view nidm files on the fly. Here we will run an example using a local file (nidm.ttl) for which the excursion set maps are served from a webserver (neurovault) and the full paths represented in the excsetmap_location parameter in the turtle file. This use case coincides with downloading a nidm.ttl and wanting to look at (remotely hosted) maps.

nidmviewer neurovault/nidm.ttl --port 8833
Starting up the nidmviewer!
Found results matching query.
/tmp/tmpuwfuszb9
Serving nidmviewer at port 8833
127.0.0.1 - - [24/Jan/2018 12:03:43] "GET /pycompare.html HTTP/1.1" 200 -
Created new window in existing browser session.

The browser should open up automatically to the url.

But what if you have an entire (local) set of nidm files and images? We have a lot of images locally in the fsl folder:

ls fsl/
ContrastStandardError_T001.nii.gz  DesignMatrix.csv          GrandMean.nii.gz                 MNI152_T1_2mm_brain.nii.gz       rendered_thresh_zstat1.png  TStatistic_T001.nii.gz
ContrastStandardError_T002.nii.gz  DesignMatrix.png          index.html                       MNI152_T1_8mm_brain_mask.nii.gz  rendered_thresh_zstat2.png  TStatistic_T002.nii.gz
Contrast_T001.nii.gz               ExcursionSet_T001.nii.gz  Mask.nii.gz                      nidm.provn                       ResidualMeanSquares.nii.gz  ZStatistic_T001.nii.gz
Contrast_T002.nii.gz               ExcursionSet_T002.nii.gz  MNI152_T1_2mm_brain_mask.nii.gz  nidm.ttl                         SearchSpaceMask.nii.gz      ZStatistic_T002.nii.gz

and if you look in the examples/fsl/nidm.ttl you will see paths to files. If you naively try to serve them from (somewhere other than the same folder they live in) you are going to get a bunch of 404s. Please cd into the folder before you do this, so the web root is where the files are found:

nidmviewer fsl/nidm.ttl --port 8811

img/example.png

You can see the basic usage by typing the command:

usage: nidmviewer [-h] [--base BASE] [--port PORT]
                  [--columns_to_remove COLUMNS_TO_REMOVE]
                  ttl

command line or server tool to view or compare nidm results.

positional arguments:
  ttl                   List of comma separated ttl files to parse.

optional arguments:
  -h, --help            show this help message and exit
  --base BASE           base image (standard brain map) to use for the viewer
                        background.
  --port PORT           PORT to use to serve nidmviewer (default 8088).
  --columns_to_remove COLUMNS_TO_REMOVE
                        Comma separated list of columns to remove from viewer.
usage: nidmviewer [-h] [--base BASE] [--port PORT]
                  [--columns_to_remove COLUMNS_TO_REMOVE]
                  ttl

command line or server tool to view or compare nidm results.

positional arguments:
  ttl                   List of comma separated ttl files to parse.

optional arguments:
  -h, --help            show this help message and exit
  --base BASE           base image (standard brain map) to use for the viewer
                        background.
  --port PORT           PORT to use to serve nidmviewer (default 8088).
  --columns_to_remove COLUMNS_TO_REMOVE
                        Comma separated list of columns to remove from viewer.

If you need more substantial customization, it's recommended to use the python functions to generate your own html.

Python

see an example. This example will generate a snippet of code that you can save as an index.html file, and will render served alongside the images in the examples/fsl folder.

Many Thanks

please submit feedback and requests or see the demo