Purpose: Take the raw Dicoms from a Siemen's scanner and transfer them to NIFTI format, and do some basic preproccessing depending on the scan type. Parameters: i=input directory (where the raw subject data folder resides) o=output directory (where the NIFTI data will go) l=user made .csv file (contains subject information) v=user made .csv file (contains scan information) S=quotation ("") enclosed list of scans to reconstruct (optional, default is complete all scans) Produces: Dependent on scan being processed, but the general output will resemble the following directory/file structure.

Definitions ${Scan}= placeholder for scan type, what you would actually see is something like slicesdir_MPRAGE, slicesdir_DTI, etc. ${num}= subject number (conventionally) like 10, 1001, 423, etc. ${cond}= useful when participants have multiple visits (i.e. pre/ post/) Func.png= pictures of the relative and absolute motion parameters for each functional scan for each subject Scan.png= pictures of the scan at various slices to make sure nothing looks grossly wrong with the image. Scan_RPI.nii.gz= the scan in NIFTI format and RPI orientation Dicoms= The original raw data, in case you need to reconstruct it differently

TEXT REPRESENTATION OF OUTPUT STRUCTURE OutputDir -> Func_Motion_check -> Func.png -> slicesdir_${Scan} -> Scan.png -> sub${num}->${Cond} -> ${Scan} -> Scan_RPI.nii.gz -> Raw -> Dicoms Preconditions: dependent on the following programs being installed and defined in your $PATH variable afni http://afni.nimh.nih.gov/afni/download/afni/releases fsl http://fsl.fmrib.ox.ac.uk/fsldownloads/fsldownloadmain.html freesurfer https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall dcm2niix https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#General_Usage

Notes on how to organize the .csv files scanlog.csv example Column1 Column2 Column3 Column4 SUB_ID SCAN_DATE CONDITION PROCESSED? 10 20150923 pre 1 10 20151023 post 0

Definitions SUB_ID= the subject ID SCAN_DATE= more specifically the name of the Raw data folder for that subject CONDITION= whether it's pre or post or session1,2,3, etc. PROCESSED?= whether the subject's scans have been reconstructed (0=not done, 1=done)

scanvol.csv example Column1 Column2 SCAN_TYPE SCAN_VOLS MPRAGE 176 DTI 70 REST 315

Definitions SCAN_TYPE= this is the type of scan that was completed in your study SCAN_VOLS= this is the number of expected dicoms for that scan (the script will not reconstruct scans with the wrong number of dicoms)