L-Measure Command Line Usage

This Document will help you to understand different input options in L-Measure.
Structure of Input:
Optional parameter = <>
Mandatory Parameter = []
<-l..> <-f..> <-f,f..> <-s /path to output file> <-p,-C,-w,-x,-t,-R,-G,-M> [/path to input file]
The minimum selection should include:
(a) Measurement: one input file and one function
(b) Conversion: one input file and one of the flags (-p. C, -w,-x, -t)
(c) Group comparisons: one function, two input directories containing two groups of SWC files.

NOTE:

1) When a single function is selected.
To compute Diameter in L-Measure we need to give following command in command prompt:
Win: Lm.exe f9,0,0,10.0 s </Path to output file> </Path to input file>
Linux: ./Lmeasure f9,0,0,10.0 s</Path to output file></Path to input file>
Input parameters: -f9,0,0,10.0
-f9 : the Diameter function is selected.
0 : sets default value to 0, which denotes absolute values instead of average.
0 : sets default value to 0, which denotes no of bins/size of width
10.0 : sets default value for no of bins.
-s : is for the path of the output file.


2) When Double Distribution is calculated.
To compute Diameter in L-Measure we need to give following command in command prompt:
Win: Lm.exe f1,f24,0,0,10.0 s</Path to output file> </Path to input file>
Linux: ./Lmeasure f1,f24,0,0,10.0 s</Path to output file> </Path to input file>
Other input options are same as single function except for the extra function parameter that selects the second function B that is measured in comparison with the first function A. L-Measure will return a series of values of Function A Vs Function B
e.g.
# extracting the values of Contraction in comparison of N_stems.
-f1 : Function A
f24: Function B
-f1,f24,0,0,10.0
-sD:\Komal\Temp\Testing\Testcases_for_win_v6.0\RawData\Lmout.txt
D:\Komal\Final_TestBed\Amira\JBC4L.am


3) Other different Type of conversions and functions.
If we open Lmin.txt we see the input flags that denote the operation to be performed on the input file provided. Here are some input flags that might help you to recognize how to read Lmin.txt:
NOTE: all the flags are case sensitive

-R is for Raw data for function/s
Which is used to compute Compartment level functions.
e.g.
# extracting the raw values along with the standard output for length function for the given input file.
-f11,0,0,10.0
-sD:\Komal\Temp\Testing\Testcases_for_win_v6.0\RawData\Lmout.txt -R
D:\Komal\Final_TestBed\Amira\JBC4L.am

-G is for Global Data
Global Data allows the user to perform Global study on multiple neurons.
e.g.
# extracting the values from all input files and treating them as one neuron to compute width and diameter.
-f5,0,0,10.0 -f9,0,0,10.0
-sD:\Komal\Temp\Testing\Testcases_for_win_v6.0\GlobalData\Lmout.txt -G
D:\Komal\Final_TestBed\Amira\JBC4L.am
D:\Komal\Temp\Testing\Final_TestBed\SWC\10gaaSTD.swc

-M is when statistic is selected
In this example Group1 is given the SWC directory and Group2 is also given the SWC directory. A two group stat test is performed on these two groups of neurons to see if there are any significant differences between them w.r.t the selected morphometrics that are chosen in the function panel.
e.g.
# extracting the statistical differences between the selected input directories with respect to the function width.
-f5,0,0,10.0
-sD:\Komal\Temp\Testing\Testcases_for_win_v6.0\Statistic\Lmout.txt -M
D:\Komal\Temp\Testing\Testcases_for_win_v6.0\Statistic\1286908626593\dir1\
D:\Komal\Temp\Testing\Testcases_for_win_v6.0\Statistic\1286908626593\dir2\

-l is for specificity
Using specificity it is possible to select just a part of the neuron to be analyzed
e.g.
# Extracting specific part of the input neuron and analyzing for height. -l1,2,2,1.0 -l1,1,8,4.0
-f6,0,0,10.0
-sD:\Komal\Temp\Testing\Testcases_for_win_v6.0\Specificity\Lmout.txt
D:\Komal\Final_TestBed\SWC\59VS3.swc

-t is for subtree
This option is to generate the sub trees or analyze the generated sub trees. The sub trees will be generated in SWC format.
- If "Generate Subtrees" option is selected, the sub trees of the input neuron is created in sub_trees_dir" folder in the same location as the input neuron file.
- If "Analyze Subtrees" is selected, only sub trees information is displayed in the Go panel. No sub trees are stored in physical location.
e.g.
# extracts the subtree from the input neuron.
-sD:\Komal\Temp\Testing\Testcases_for_win_v6.0\Subtree\Lmout.txt -t
D:\Komal\Temp\Testing\Final_TestBed\SWC\10gaaSTD.swc

-p is for conversion to SWC format.
Using SWC Conversion a copy of all neurons loaded in the Input panel is converted to SWC format and saved in the same directory of the original files
e.g.
# extracting the data from the input file and will convert it to SWC format.
-sD:\Komal\Temp\Testing\Testcases_for_win_v6.0\SWC_Conversion\Lmout.txt -p
D:\Komal\Final_TestBed\Neurolucida\allman\Source-Version\02b_pyramidal1aACC.ASC

-w is for conversion to wrl format.
Using wrl Conversion a copy of all neurons loaded in the Input panel is converted to WRL format and saved in the same directory of the original files
e.g
# extracting the data from the input file and will convert it to WRL format.
-sD:\Komal\Temp\Testing\Testcases_for_win_v6.0\WRL_Conversion\Lmout.txt -w
D:\Komal\Temp\Testing\Final_TestBed\Soma\No+Soma\A1-May29-IR1-1A.swc.CNG.swc

-x is for conversion to dxf format.
Using dxf Conversion a copy of all neurons loaded in the Input panel is converted to DXF format and saved in the same directory of the original files
e.g
# extracting the data from the input file and will convert it to DXF format.
-sD:\Komal\Temp\Testing\Testcases_for_win_v6.0\DXF_Conversion\Lmout.txt -x
D:\Komal\Final_TestBed\Amira\JBC4L.am

-C do PCA
Principal Component Analysis only applies to 3 morphological functions viz. Height, Width, and Depth. It shifts the long axis of the neuron perpendicular to the x-axis.
e.g.
# extracting the co-ordinates and shift it to display width. -f5,0,0,10.0
-sD:\Komal\Temp\Testing\Testcases_for_win_v6.0\Random\Lmout.txt -C
D:\Komal\Final_TestBed\SWC\71Slat1.swc
D:\Komal\Final_TestBed\SWC\71Slat1.swc

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