some minor changes including getting subtract corpus to produce an

average image

bash/sort_invivo

@@ -20,7 +20,7 @@ for d in $1/*; do
     image_name=`basename $dataset`
     structure=${image_name%%.*}
     num_encodings=${image_name#*.}
-    num_encodings=${num_encodings%.*}
+    num_encodings=${num_encodings%%.*}
     parent_dir=$destination/$structure/$subject/$num_encodings
     mkdir -p $parent_dir
     count=1

bash/subtract_corpus

@@ -24,13 +24,16 @@ for subject_dir in $data_dir/corpus_callosum/*; do
             num_width=`fibre_info $run_dir/samples.tst | grep exp_num_width_sections | awk '{print $2}'`
             obs_image=`fibre_info $run_dir/samples.tst | grep obs_image | awk '{print $2}'`
             obs_image=$REFERENCE_DIR/${obs_image#*params/image/reference/}
-            img_dims="\"`mrinfo $obs_image | grep Dimensions: | awk '{print $2 " " $4 " " $6}'`\""
-            img_vox_lengths="\"`mrinfo $obs_image | grep 'Voxel size:' | awk '{print $3 " " $5 " " $7}'`\""
-            img_offset="\"`mrinfo $obs_image | grep --after-context=2 'Transform:' | xargs echo | awk '{print $5 " " $9 " " $13}'`\""
+            img_dims="\"`mrinfo $obs_image | grep Dimensions: | awk '{print $2 "," $4 "," $6}'`\""
+            img_vox_lengths="\"`mrinfo $obs_image | grep 'Voxel size:' | awk '{print $3 "," $5 "," $7}'`\""
+            img_offset="\"`mrinfo $obs_image | grep --after-context=2 'Transform:' | xargs echo | awk '{print $5 "," $9 "," $13}'`\""
             gradient_file=${obs_image%.mif}.grad
             mrinfo $obs_image -gradient $gradient_file
-            echo generate_image $run_dir/last.tct $run_dir/last.mif -img_dims $img_dims -img_vox_lengths $img_vox_lengths -img_offset $img_offset -exp_num_length_sections $num_length -exp_num_width_sections $num_width -diff_encodings_location $gradient_file
+            #generate_image $run_dir/last.tct $run_dir/last.mif -img_dims $img_dims -img_vox_lengths $img_vox_lengths -img_offset $img_offset -exp_num_length_sections $num_length -exp_num_width_sections $num_width -diff_encodings_location $gradient_file
             #echo $img_dims - $img_vox_lengths - $img_offset - $num_length - $num_width
         done
+        num_runs=`ls $data_dir/corpus_callosum/$subject/$dw | wc | awk '{print $1}'`
+        #echo $subject - $dw - $num_runs
+        mradd $data_dir/corpus_callosum/$subject/$dw/*/last.mif - | mrmath $num_runs -divide $data_dir/corpus_callosum/$subject/$dw/avg_last.mif
     done
 done

matlab/add_mri_slice_to_plot.m

@@ -7,15 +7,15 @@ function add_mri_slice_to_plot(image_location, x_slice, y_slice, z_slice)
     img_limit = offset + img.vox(1:3) .* (img.dim(1:3) - 1);
 
     if any(x_slice > img_limit(1)) || any(x_slice < offset(1))
-     error(['Slice positions (' num2str(x_slice) ') out of bounds of the image (' num2str(offset(1)) ' -> ' num2str(img_limit(1)) ').'])
+     error(['X slice position (' num2str(x_slice) ') out of bounds of the image (' num2str(offset(1)) ' -> ' num2str(img_limit(1)) ').'])
     end
 
     if any(y_slice > img_limit(2)) || any(y_slice < offset(2))
-     error(['Slice positions (' num2str(y_slice) ') out of bounds of the image (' num2str(offset(2)) ' -> ' num2str(img_limit(2)) ').'])
+     error(['Y slice position (' num2str(y_slice) ') out of bounds of the image (' num2str(offset(2)) ' -> ' num2str(img_limit(2)) ').'])
     end
 
     if any(z_slice > img_limit(3)) || any(z_slice < offset(3))
-     error(['Slice positions (' num2str(z_slice) ') out of bounds of the image (' num2str(offset(3)) ' -> ' num2str(img_limit(3)) ').'])
+     error(['Z slice position (' num2str(z_slice) ') out of bounds of the image (' num2str(offset(3)) ' -> ' num2str(img_limit(3)) ').'])
     end
 
     [X,Y,Z]=meshgrid(offset(1):img.vox(1):img_limit(1),...

matlab/tracts2strands.m

@@ -37,7 +37,7 @@
       num_strands = round(sqrt(strands_per_acs * acs));    
   end
 
-  width_fractions = ones(length(tracts),1) ./ num_strands;
+  width_fractions = ones(size(tracts,1),1) ./ num_strands;
 
   if num_strands < 0
     error(['''-num_strands'' must be greater than zero (' num2str(num_strands) ').']);