Wednesday, 25 March 2015

DTI preparation for TBSS analysis

Before anything else you need to be sure that the data you need (diffusion and T1 images) have all been retrieved from Dougal into /data/blinded and contain no duplicates.
1) LOGIN IN TO ONE OF THE LINUX SERVERS (nanlnx1, nanlnx2,...)
% ssh kxxxxxxx@nanlnx1.iop.kcl.ac.uk
2) ADD THE NBL MODULE (THIS WILL SET UP YOU ENVIRONMENT SO YOU CAN RUN THE PIPELINE COMMANDS)
%  module add /home/k1339392/software/nbl /etc/nblmodule
3) CREATE THE FOLDERS FOR YOUR PROJECT (i.e. DRUM_PROJECT)
% mkdir ~/DRUM_PROJECT
% mkdir ~/DRUM_PROJECT/nandata
% mkdir ~/DRUM_PROJECT/dtidata
% mkdir ~/DRUM_PROJECT/expdtidata
% cd ~/DRUM_PROJECT
% ls
4) GET THE DATA FROM DOUGAL (add new folders with NIFTI data to ./nandata with NIFTI data)
% getnandata /data/blinded/CNSCNSD ./nandata DRUMPILOT01
% ls ./nandata
5) PREPARE DTI DATA FOR PREPROCESSING ( adds *.nii.gz *.bvec *.bval _mask.nii.gz files to ./dtidata). Use -C option if your data was acquired in the old CNS scanner using the 32 directions pulse sequence (i.e. BRCATLAS and MIAMRC projects).
% prepdti -C  ./nandata ./dtidata DRUMPILOT01 DTI_2mm_60B1500_FDA
% ls ./dtidata
6) PREPARE T1 DATA REQUIRED FOR EPI CORRECTION (adds new _T1.nii.gz _T1_mask.nii.gz files to ./dtidata)
% prept  ./nandata ./dtidata DRUMPILOT01 MPRAGE
7) RUN EXPLORE DTI PREPROCESSING SCRIPT (creates new *.mat *_EPI.mat files in ./expdtidata )
SM/EC CORRECTION ONLY
% expdticorr -R  ./dtidata ./expdtidata DRUMPILOT01 _SMEC
% ls ./expdtidata
SM/EC/EPI CORRECTION
% expdticorr -E  -R  ./dtidata ./expdtidata DRUMPILOT01 _EPI
% ls ./expdtidata

The final result will be a new file in ./expdtidata called DRUMPILOT01_[EPI/SMEC].mat. This file can only be opened with ExploreDTI. Using Explore DTI you will be able to generate any kind of diffusion images/maps you need, including of course tractography datasets.


See DTI pipeline document for more detail

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