using the try8_scaled surface mesh, and the Feb 2008 svas
note that the try8 surface mesh is rough, due to working around this bug by scaling: http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg01543.html
| composite | meaning all genes (actually, just all coronal genes) | ||||
| try8.5_scaled | using the try8 surface mesh, scaled x1000, and the Feb 2008 svas | ||||
| gs | mapping algorithm "gs" (Gaussian), with parameters: | ||||
| 2.2 | gs param: neighbor cube size (mm). | ||||
| 10 | gs param: value for sigma norm | ||||
| .1 | gs param: value for sigma tang. | ||||
| 1.1 | gs param: value for norm below cutoff (mm). | ||||
| .5 | gs param: value for norm above cutoff (mm). | ||||
| .5 | gs param: value for tang cutoff (mm). |
surfaceMeshName=try8.5_scaled
topology_file=Mouse.aba.R.topology_file_367.2007-08-28.23460.topo
fiducial_coord_file=Mouse.aba.R.coordinate_file_369.2007-08-28.23460.coord
mapping_alg_args=gs_2.2_10_.1_1.1_.5_.5
mapped_metric_files_dir=mapped_metric_files_col8_right_$mapping_alg_args
# /l/aba/niis from Sep 2008; they were based on svas
for f in /l/aba/niis/*_col8_right.nii; do echo Processing $f >> metric_mapping_progress.txt; caret_command -volume-map-to-surface $fiducial_coord_file $topology_file \"\" `basename $f .nii`_$mapping_alg_args.metric METRIC_GAUSSIAN $f -g 2.2 10 .1 1.1 .5 .5 2>&1 >> metric_mapping_progress.txt; done
mkdir $mapped_metric_files_dir
mv [0-L]*_col8_right_$mapping_alg_args.metric $mapped_metric_files_dir
mv *_col8_right_$mapping_alg_args.metric $mapped_metric_files_dir
caret_command -metric-composite composite_0-B_${surfaceMeshName}_$mapping_alg_args.metric $mapped_metric_files_dir/[0-B]*.metric
caret_command -metric-composite composite_0-F_${surfaceMeshName}_$mapping_alg_args.metric composite_0-B_${surfaceMeshName}_$mapping_alg_args.metric $mapped_metric_files_dir/[C-F]*.metric
caret_command -metric-composite composite_0-L_${surfaceMeshName}_$mapping_alg_args.metric composite_0-F_${surfaceMeshName}_$mapping_alg_args.metric $mapped_metric_files_dir/[G-L]*.metric
caret_command -metric-composite composite_0-R_${surfaceMeshName}_$mapping_alg_args.metric composite_0-L_${surfaceMeshName}_$mapping_alg_args.metric $mapped_metric_files_dir/[M-R]*.metric
caret_command -metric-composite composite_0-S_${surfaceMeshName}_$mapping_alg_args.metric composite_0-R_${surfaceMeshName}_$mapping_alg_args.metric $mapped_metric_files_dir/S*.metric
caret_command -metric-composite composite_0-T_${surfaceMeshName}_$mapping_alg_args.metric composite_0-S_${surfaceMeshName}_$mapping_alg_args.metric $mapped_metric_files_dir/T*.metric
caret_command -metric-composite composite_${surfaceMeshName}_$mapping_alg_args.metric composite_0-T_${surfaceMeshName}_$mapping_alg_args.metric $mapped_metric_files_dir/[U-z]*.metric
perl -e 's/(tag-column-name \d+ [a-zA-Z0-9_\*-\.]+).nii -.*/\1/;' -pi composite_${surfaceMeshName}_$mapping_alg_args.metric
perl -e 'while (<>) {if (/tag-column-name \d+ (.*)_col8_right/) {print $1 . "\n";}}' < composite_${surfaceMeshName}_$mapping_alg_args.metric > gene_list_${surfaceMeshName}_$mapping_alg_args.txt
#cat gene_list_${surfaceMeshName}_$mapping_alg_args.txt | sort | uniq > gene_list_${surfaceMeshName}_$mapping_alg_args.txt.temp
#mv gene_list_${surfaceMeshName}_$mapping_alg_args.txt.temp gene_list_${surfaceMeshName}_$mapping_alg_args.txt
cp composite_${surfaceMeshName}_$mapping_alg_args.metric composite_${surfaceMeshName}_${mapping_alg_args}_txt.metric
caret_command -file-convert -format-convert ASCII composite_${surfaceMeshName}_${mapping_alg_args}_txt.metric
perl -e 'undef $/; $file = <>; $file =~ s/.*tag-BEGIN-DATA\n//s; print $file' < composite_${surfaceMeshName}_${mapping_alg_args}_txt.metric > ${surfaceMeshName}_right_${mapping_alg_args}.txt