For Newbies

I'm new to the lab, what do I do?

First, make sure you have MATLAB installed. I prefer if your OS is Ubuntu Linux 64-bit, or at least that you have access to it. Depends on what you are doing you will need to download different software for analysis. Here are links to the usual software and toolboxes we use. Make sure you download the latest versions.

It is your responsibility to install the software yourself.

• DCM2NII

• SPM

• FSL

• AFNI

• MRtrix

• CONN Toolbox

All DICOM raw data must be kept in a separate folder and must not be used. All DICOM raw data must be anonymized in a new separate DICOM_ANON folder with this structure: /root/data/dicom_anon/subject_id/sequence

Example: /media/INP/project_addiction/data/dicom_anon/036/t1

To anonymize Dicoms, use this python script https://github.com/chop-dbhi, then you can use or change my script https://github.com/GarzaLab/script_examples/blob/master/dicomanon.sh