changes to readme

README.md

@@ -73,42 +73,37 @@ NeuroImage, 76(1), 400-411. DOI: 10.1016/j.neuroimage.2013.03.015
 
 XTRACT automatically detects if $SGE_ROOT is set and if so uses FSL_SUB. For optimal performance, use the GPU version!!!!
 
-Outputs of XTRACT
+**Outputs of XTRACT**
 
 Under <outputDir>:
 
 - "commands.txt" - XTRACT processing commands
 - "logs" - directory containing the probtrackx log files
 - "tracts" - directory continaing tractography results
--- "<tractName>" - directory per tract, each continaing:
--- "waytotal" - txt file continaing the number of valid streamlines
--- "density.nii.gz" - nifti file containing the fibre probability distribution
--- "density_lenths.nii.gz" - nifti file containing the fibre lengths, i.e. each voxel is the average streamline length - this is the "-ompl" probtrackx option
--- "densityNorm.nii.gz" - nifti file continaing the waytotal normalised fibre probability distribution (the "density.nii.gz" divided by the total number of valid streamlines)
--- If the protocol calls for reverse-seeding:
---- "tractsInv" - directory continaing the above for the seed-target reversed run
---- "sum_waytotal" and "sum_density.nii.gz" - the summed waytotal and fibre probability distribution
--- If the "-native" option is being used:
---- "masks" - directory
---- "<tractName>" - directory per tract continaing the native space protocol masks
+  - "<tractName>" - directory per tract, each continaing:
+  - "waytotal" - txt file continaing the number of valid streamlines
+  - "density.nii.gz" - nifti file containing the fibre probability distribution
+  - "density_lenths.nii.gz" - nifti file containing the fibre lengths, i.e. each voxel is the average streamline length - this is the "-ompl" probtrackx option
+  - "densityNorm.nii.gz" - nifti file continaing the waytotal normalised fibre probability distribution (the "density.nii.gz" divided by the total number of valid streamlines)
+  - If the protocol calls for reverse-seeding:
+    - "tractsInv" - directory continaing the above for the seed-target reversed run
+    - "sum_waytotal" and "sum_density.nii.gz" - the summed waytotal and fibre probability distribution
+  - If the "-native" option is being used:
+    - "masks" - directory
+    - "<tractName>" - directory per tract continaing the native space protocol masks
 
 The primary output is the "densityNorm.nii.gz" file.
 
-Pre-processing
+**Pre-processing**
 
 Prior to running XTRACT, you must complete the FDT processing pipeline:
 
-Brain extraction using BET
-
-Susceptibility distortion correction using topup (only if spin-echo fieldmaps have been acquired - if you don't have these, skip to step 3)
-
-Eddy current distortion and motion correction using eddy
-
-Fit the crossing fibre model using bedpostx
-
-Registration to standard space (MNI152), see the FDT pipeline
-
-Your data should now be ready to run XTRACT!
+1. Brain extraction using BET
+2. Susceptibility distortion correction using topup (only if spin-echo fieldmaps have been acquired - if you don't have these, skip to step 3)
+3. Eddy current distortion and motion correction using eddy
+4. Fit the crossing fibre model using bedpostx
+5. Registration to standard space (MNI152), see the FDT pipeline
+6. Your data should now be ready to run XTRACT!