Hi Carolina,

great you succeeded in the installation!

The scripts are intended for batch processing the datasets in preparation for functional connectivity analyses (in fact they can also do these for you). Once you have the data set up in XNAT, you can select subjects you want to process (e.g., based on IQ or Age), and export them again. Then you can apply the scripts to these datasets.

For practice reasons, I would suggest you to download one of the Lite releases as these already come in an easy structure (searching for variables of interest is a bit harder though as you have to search through a spreadsheet).

Finally, the scripts are intended for use with NIFTI files, so if you downloaded DICOM (which is perfectly fine), you will have to convert the datasets to .nii first. You can use dcm2nii from mricron (also available on nitrc) for that.

The scripts are bash scripts. You can either run them within the virtual machine or within any UNIX (Mac, Linux, or Cygwin for windows) environment. You just need access to your data. That is for instance why we have you make the host folder during setup so data from the virtual machine would be also available on your 'actual' computer.

Hope this helps,
Maarten