TBSS preparation

ExploreDTI to set up files for RA/AD

Open matlab by typing matlab into terminal

Go up in current directory to find the folder ‘exploredti’ then go into it and drag and drop ‘source’ and ‘MainExploreDTI’ into terminal.

Type MainExploreDTI

-          ‘plugins’ – ‘export stuff to *.nii files’ – select ‘multiple’- select ‘FA/largest eigenvalue’-  select ‘MD/Radial/transverse diffusivity’ – ‘ok’

S    Select file containing mat files and then select files to save the files in.

- - This will produce nifti files for the measures that you have selected.

     TBSS

      http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS/UserGuide

All data should be in NIFTI format and corrected for the effects of eddy current distortions and head motion.

Make directories called 'TBSSmain' and inside that 'mytbss'
Copy FA nifti files into mytbss
Navigate into 'mytbss'

Preprocessing

-    %tbss_1_preproc *.nii
-         % tbss_2_reg -T 

-         %  tbss_3_postreg –S

-          %  tbss_4_prestats 0.2

n    These commands perform a non-linear registration and affine transformation into MNI space using the non-linear registration tool. This creates mean FA and skeletonised images.

S   See TBSS UserGuide for other options.

Freesurfer longitudinal processing stream

https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial

1. Cross-sectionally process your data (recon-all)

2. Create template for all timepoints for each subject.

recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all

3. Longitudinally process all timepoints

  recon-all -long <tpNid> <templateid> -all

4. Inspect the base and longitudinal data