reverted get_dw_response back to median from max as this seems to be

picking up edge effects
tclose · Dec 25, 2012 · a6f8358 · a6f8358
1 parent 46ca68d
commit a6f8358
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Showing 9 changed files with 5 additions and 8 deletions.
diff --git a/bash/get_dw_response b/bash/get_dw_response
@@ -38,13 +38,10 @@ gen_WM_mask $dwi_file ${pfx}mask.mif - | threshold - ${pfx}wm_mask.mif -abs $WM_
 dwi2tensor $dwi_file - | tensor2FA - - | mrmult - ${pfx}wm_mask.mif - | threshold - ${pfx}sf_mask.mif -abs $SF_FA_THRESHOLD
 
 # Mask single_fibre mask with whole brain mask 
-estimate_response $dwi_file ${pfx}sf_mask.mif $output -lmax 8 -normalise
-
-# For debugging
-#echo "get_b0 $dwi_file ${pfx}sf_mask.mif"
+#estimate_response $dwi_file ${pfx}sf_mask.mif $output -lmax 8 -normalise
 
 # Save the average b0 to file for use in scaling the base intensity of the expected image
-get_b0 $dwi_file ${pfx}sf_mask.mif > ${output_base}.b0.$output_ext
+get_b0 $dwi_file ${pfx}sf_mask.mif -method median > ${output_base}.b0.$output_ext
 
 # Cleaning up temporary files
 rm "${pfx}"*

diff --git a/params/image/reference/donald/anat.nii b/params/image/reference/donald/anat.nii
diff --git a/params/image/reference/donald/anat.nii b/params/image/reference/donald/anat.nii
@@ -0,0 +1 @@
+/home/t/tclose/reference/baftrs/donald/anat.nii
diff --git a/params/image/reference/donald/dwi.mif b/params/image/reference/donald/dwi.mif
diff --git a/params/image/reference/donald/dwi.mif b/params/image/reference/donald/dwi.mif
@@ -0,0 +1 @@
+/home/t/tclose/reference/baftrs/donald/dwi.mif
diff --git a/params/image/reference/donald/response.txt b/params/image/reference/donald/response.txt
diff --git a/params/image/reference/heath/anat.nii b/params/image/reference/heath/anat.nii
diff --git a/params/image/reference/heath/anat.nii b/params/image/reference/heath/anat.nii
@@ -0,0 +1 @@
+/home/t/tclose/reference/baftrs/heath/anat.nii
diff --git a/params/image/reference/heath/dwi.mif b/params/image/reference/heath/dwi.mif
diff --git a/params/image/reference/heath/dwi.mif b/params/image/reference/heath/dwi.mif
@@ -0,0 +1 @@
+/home/t/tclose/reference/baftrs/heath/dwi.mif
diff --git a/params/image/reference/lisa/anat.nii b/params/image/reference/lisa/anat.nii
diff --git a/params/image/reference/lisa/anat.nii b/params/image/reference/lisa/anat.nii
@@ -0,0 +1 @@
+/home/t/tclose/reference/baftrs/lisa/anat.nii
diff --git a/params/image/reference/lisa/dwi.mif b/params/image/reference/lisa/dwi.mif
diff --git a/params/image/reference/lisa/dwi.mif b/params/image/reference/lisa/dwi.mif
@@ -0,0 +1 @@
+/home/t/tclose/reference/baftrs/lisa/dwi.mif
diff --git a/python/hpc/baftrs_in_action.py b/python/hpc/baftrs_in_action.py
@@ -20,9 +20,10 @@
                 os.path.join('donald', 'init3.tct'),
                 os.path.join('donald', 'init4.tct'),
                 os.path.join('donald', 'init5.tct')]
-INIT_CONFIGS = [os.path.join('donald', 'init1.tct')]
-DATASETS = [os.path.join('donald', 'fornix.mif')] * len(INIT_CONFIGS)
+INIT_CONFIGS = [os.path.join('donald', 'rand_init.tct')]
 #DATASETS = [os.path.join('donald', 'fornix.mif'), os.path.join('heath', 'fornix.mif'), os.path.join('lisa', 'fornix.mif')]
+DATASETS = [os.path.join('donald', 'fornix.mif')] * len(INIT_CONFIGS)
+DATASETS = [os.path.join('donald', 'test_image3.mif')] * len(INIT_CONFIGS)
 # Required dirs for the script to run
 REQUIRED_DIRS = ['params/image/reference', 'params/diffusion', 'params/fibre/tract/masks/mcmc/metropolis']
 # Arguments that can be given to the script
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		/home/t/tclose/reference/baftrs/donald/anat.nii