Input formats

Currently supported:

  • pyradigm’s data structures (highly recommended)

    • for advanced features of handling covariates/confounds, this is required!

  • Arbitary/user-defined format (see below)

  • CSV files (with samples along rows and features along columns)

  • Weka’s ARFF

Formats specific to neuroimaging:

  • Freesurfer

  • Subcortical volumes

  • Wholebrain Aseg stats

In development (stay tuned)

  • Freesurfer

    • cortical thickness

    • gray matter density

    • structural covariance

  • Any nibabel-readable data

  • DT-MRI features

  • task-free fMRI features

  • HCP datasets

Interfaces to Neuroimaging tools

neuropredict is aimed at interfacing with popular feature extraction algorithms such as Freesurfer, FSL and others directly - see Readers section below. However, it allows an arbitray input of features that have already been extracted via user’s own pipeline(s).

Arbitrary feature input

For custom input:

  • the user needs to save the features in a single folder for all subjects (let’s call it /project/myawsomepipeline )

    • specify it with –userdefined /project/myawsomepipeline

  • within which, features for each subject in a separate folder (named after its id specified in the meta data file)

  • in a file called features.txt. The features.txt file must contain a single floating point number per line (see below - its not comma separated),

  • and all the subject features must have an equal number of features.

Then neuropredict will automatically consolidate the features into its native pyradigm MLdataset format, ideally suited for the predictive analysis tasks.

The example for a dataset with 2 controls and 2 disease sujects with 5 features each is shown below:

$ 11:19:22 linux userdefined >>  ls -1
control-001
control-002
disease-003
disease-004
$ 11:19:30 linux userdefined >>  tree
.
|-- control-001
|   `-- features.txt
|-- control-002
|   `-- features.txt
|-- disease-003
|   `-- features.txt
`-- disease-004
    `-- features.txt

4 directories, 4 files
$ 11:19:33 linux userdefined >>  head -n 5 */features.txt
==> control-001/features.txt <==
0.868896136902
0.542305564899
0.115903893374
0.503297862357
0.564961631104

==> control-002/features.txt <==
0.868896136902
0.542305564899
0.115903893374
0.503297862357
0.564961631104

==> disease-003/features.txt <==
0.868896136902
0.542305564899
0.115903893374
0.503297862357
0.564961631104

==> disease-004/features.txt <==
0.868896136902
0.542305564899
0.115903893374
0.503297862357
0.564961631104