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
Complete documentation is available
To install
pip install nidmviewer
To install development version:
pip install git+git://github.com/vsoch/nidmviewer.git
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
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.
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.
- Papaya Viewer, we salute you!
- NeuroVault don't mess with the NeuroVault!
please submit feedback and requests or see the demo
