https://github.com/vsoch/nidmviewer
NIDM Results Viewer
https://github.com/vsoch/nidmviewer
Last synced: over 1 year ago
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NIDM Results Viewer
- Host: GitHub
- URL: https://github.com/vsoch/nidmviewer
- Owner: vsoch
- License: bsd-3-clause
- Created: 2015-10-10T23:35:32.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2018-07-05T22:42:10.000Z (about 8 years ago)
- Last Synced: 2025-04-12T12:12:01.998Z (over 1 year ago)
- Language: CSS
- Homepage: http://vsoch.github.io/nidmviewer/
- Size: 7.31 MB
- Stars: 3
- Watchers: 2
- Forks: 3
- Open Issues: 12
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
# 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](http://vsoch.github.io/font-brain) for nidm and brain imaging icons
## Documentation
Complete documentation [is available](http://nidmviewer.readthedocs.org/en/latest/)
### 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](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.
#### Python
see [an example](examples/generate_viewer.py). 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](examples/fsl) folder.
###### Many Thanks
- [Papaya Viewer](https://github.com/rii-mango/Papaya), we salute you!
- [NeuroVault](https://github.com/NeuroVault/NeuroVault) don't mess with the NeuroVault!
please [submit feedback and requests](https://github.com/vsoch/nidmviewer) or see the [demo](http://vsoch.github.io/nidmviewer)