mp-transformation.py
can be run from the command line after setting parameters in mp-transformation-config.json
. When you run the script, you only need to provide the path to the config file as an argument :
$ python mp-transformation.py "C:\\path\\to\\mp-transformation-config.json"
In addition to the parameters described in Parameter Reference, mp-transformation-config.json
requires a set of additional parameters:
rootdir
Required: String specifying the complete path to a directory where an output folder should be created
expname
Required: String specifying the experiment name that will be incorporated into output files
c1-dir
Required: String specifying the path to the directory containing the _Probabilities.files
for the structural channel
c1-key
Required: String that will serve as a key for the structural channel and will name the output files
c2-dir
Optional: Same as c1-dir
, but for an additional channel
c2-key
Optional: Same as c1-key
, but for an additional channel
c3-dir
Optional: Same as c1-dir
, but for an additional channel
c3-key
Optional: Same as c1-key
, but for an additional channel
c4-dir
Optional: Same as c1-dir
, but for an additional channel
c4-key
Optional: Same as c1-key
, but for an additional channel
twoD
A boolean value that specifies, which PCA transformation functions will be used.
True
: brain.calculate_pca_median_2d
and brain.pca_transform_2d
will be used to hold one axis constant, while the other two are realigned with PCA
False
: brain.calculate_pca_median
and brain.pca_transform_3d
will be used to transform and realign samples in all three dimensions
deltascope.mpTransformation
deltascope.mpTransformation