open-discussion > RE: Reproducibility analysis mICA
Mar 22, 2018  03:03 AM | Florian Beissner
RE: Reproducibility analysis mICA
Hi Will,

the python scripts were not made to be used outside of the toolbox. Sorry for the limited documentation.
splithalf.py only generates the folder structure for subsequent reproducibility analysis. You can execute it using

python $mICA_FOLDER/py/splithalf.py list_filename permutations out_prefix 

where "list_filename" is a list of the 4D fMRI data you want to use in your mICA, "permutations" defines the number of samplings and out_prefix sets the name of the folder.

The script that does all the real work (cross-correlation matrix -> hungarian sorting -> mean reproducibility -> export results as text table and graphical plot) is ic_corr.py. You invoke it like this

python $mICA_FOLDER/py/ic_corr.r in_prefix samples dims [just_read]

Here, "in_prefix" is the name of the folder, whose sub-folders should be organized like this:

in_prefix/sample_0001/group1/dim1
...
in_prefix/sample_0001/group1/dimMAX
in_prefix/sample_0001/group2/dim1
...
in_prefix/sample_0001/group2/dimMAX
in_prefix/sample_0002/group1/dim1
...
...
in_prefix/sample_MAX/group2/dimMAX

"samples" refers to the number of samplings ("permutations" from above).
"dims" defines a range of ICA dimensionalities that you want to include in the analysis. Of course they all need to be there. Input can be e.g. "5-100".
"[just_read]" 0 is default here. You can use 1 if you have previously calculated cross-correlation files. It will then skip fsl_cc.

Hope the helps,

Florian

P.S.: If you are using MELODIC, i propose to re-run your mICAs using the toolbox. It is much easier and offers extra functionality.

Originally posted by Will Khan:
Hi, 

I have performed a masked ICA using melodic with the HCP dataset outside of the mICA toolbox, but I would like to have some more information regarding the splithalf.py script please.

Could you please tell me what input the script requires? I have attempted to look for this in the documentation but this mostly describes the use of the GUI. 

I have previously provided the 4d melodic IC file without success. An example would be greatly appreciated! 

Thanks very much, 

Cheers, 

Will

Threaded View

TitleAuthorDate
Will Khan Mar 21, 2018
RE: Reproducibility analysis mICA
Florian Beissner Mar 22, 2018
Will Khan Mar 26, 2018
Tawfik Moher Alsady Mar 27, 2018
Will Khan Mar 28, 2018
Will Khan Mar 28, 2018
Tawfik Moher Alsady Mar 29, 2018
Will Khan Apr 4, 2018
Tawfik Moher Alsady Apr 9, 2018
Will Khan Apr 9, 2018