From b16da6f3fd8f315111826afecc461850f93770a4 Mon Sep 17 00:00:00 2001 From: davegrays Date: Wed, 23 Mar 2016 14:46:08 -0700 Subject: [PATCH] reduce WM erosion for RF estimation With 3 erosion steps, corpus callosum is excluded along with most of WM, and only ~50 voxels above FA>0.7 remain. According to MRtrix developers there should be at least a few hundred FA>0.7 voxels, mostly in the CC. --- cmp/stages/diffusion/reconstruction.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cmp/stages/diffusion/reconstruction.py b/cmp/stages/diffusion/reconstruction.py index 38c44ed..d9090d6 100644 --- a/cmp/stages/diffusion/reconstruction.py +++ b/cmp/stages/diffusion/reconstruction.py @@ -491,7 +491,7 @@ def create_mrtrix_recon_flow(config): if config.local_model: # Compute single fiber voxel mask mrtrix_erode = pe.Node(interface=mrtrix.Erode(),name="mrtrix_erode") - mrtrix_erode.inputs.number_of_passes = 3 + mrtrix_erode.inputs.number_of_passes = 1 mrtrix_mul_eroded_FA = pe.Node(interface=MRtrix_mul(),name='mrtrix_mul_eroded_FA') mrtrix_mul_eroded_FA.inputs.out_filename = "diffusion_resampled_tensor_FA_masked.mif" mrtrix_thr_FA = pe.Node(interface=mrtrix.Threshold(),name='mrtrix_thr') @@ -772,4 +772,4 @@ def create_gibbs_recon_flow(config): (inputnode,gibbs_node,[("diffusion_resampled","dwi")]), (gibbs_node,outputnode,[("recon_file","recon_file")]) ]) - return flow \ No newline at end of file + return flow