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)
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).
% ls ./dtidata
6) PREPARE T1 DATA REQUIRED FOR EPI CORRECTION (adds new
_T1.nii.gz _T1_mask.nii.gz files to ./dtidata)
7) RUN EXPLORE DTI PREPROCESSING SCRIPT
(creates new *.mat *_EPI.mat files in ./expdtidata )
% ls ./expdtidata
SM/EC/EPI CORRECTION
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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