Added some documentation and example scripts

examples/README.md

@@ -0,0 +1,7 @@
+## Example scripts for various subtools
+
+* `real_tests` - tests with real data
+* `synthetic_tests` - tests with synthetic data
+* `validation_dataset` - validation dataset for longitudinal pipeline
+
+

examples/synthetic_tests/README.md

@@ -0,0 +1,6 @@
+## examples for running various pipelines with synthetic data
+
+* `test_lng_model`  -  longitudinal model creation (4D)
+* `test_model_creation` - model creation (3D)
+* `test_registration` - registration
+* `test_segmentation` - segmentation 

examples/synthetic_tests/test_model_creation/README.md

@@ -0,0 +1,16 @@
+## Model creation examples
+
+* `prepare_test_data.sh` - prepare synthetic dataset
+* `prepare_test_data_with_bias.sh` - prepare synthetic dataset with some bias field
+
+To execute examples, setup PYTHONPATH to point to the location of `ipl` directory, then run `python -m scoop -n <n> <script.py>`
+
+* `scoop_test_1.py` - create 3 symmetric models, using linear registration with 6 parameters (rigid body), 9 parameters and 12 parameters
+* `scoop_test_2.py` - create 3 non-symmetric models, using linear registration with 6 parameters (rigid body), 9 parameters and 12 parameters
+* `scoop_test_bias*.py` - generate models compensating for bias field ( linear coregistration)
+* `scoop_test_nl.py` - generate model using non-linear coregistration with minctracc, non-simmetric
+* `scoop_test_nl_sym.py` - generate model using non-linear coregistration with minctracc, simmetric
+* `scoop_test_nl_elastix.py` - generate model using non-linear coregistration with Elastix
+* `scoop_test_nl_ants.py` - generate model using non-linear coregistration with ANTs
+* `scoop_test_nl_dd.py` - generate model using non-linear coregistration with diffeomorphic demons
+* `scoop_test_nl_ldd.py` - generate model using non-linear coregistration with log-diffeomorphic demons

examples/validation_dataset/README.md

@@ -0,0 +1,6 @@
+## Validation dataset for longitudinal pipeline
+
+To run:
+* Download data using `download_validation_dataset.sh` script
+* Run pipleine  on 4 cores : `PARALLEL=4 MNI_DATAPATH=/opt/minc/share run_validation_nc.sh`
+

examples/validation_dataset/download_validation_dataset.sh

@@ -0,0 +1,5 @@
+#! /bin/sh
+
+
+wget ipl_subject43.tar.gz 
+tar zxf ipl_subject43.tar.gz

examples/validation_dataset/run_validation_nc.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-set -e
+set -e -x
 
 output_dir=$1
 
@@ -20,7 +20,6 @@ PARALLEL=${PARALLEL:-1}
 icbm_model_dir=$MNI_DATAPATH/icbm152_model_09c
 beast_model_dir=$MNI_DATAPATH/beast-library-1.1
 
-
 if [ ! -d $icbm_model_dir ];then 
     echo "Missing $icbm_model_dir"
     exit 1
@@ -31,19 +30,17 @@ if [ ! -d $beast_model_dir ];then
     exit 1
 fi
 
-pipeline_dir=$(dirname $0)/..
+pipeline_dir=$(dirname $0)/../..
 data_dir=$(dirname $0)
 
-#export PYTHONPATH=$(realpath $pipeline_dir/python)
-export PYTHONPATH=$pipeline_dir/python
-#export PATH=$pipeline_dir/bin:$PATH
+export PYTHONPATH=$pipeline_dir
 export OMP_NUM_THREADS=1
 export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
 
 ### Run pipeline for NC scan rescan data ###
-python -m scoop -vvv -n $PARALLEL $pipeline_dir/python/iplLongitudinalPipeline.py \
+python -m scoop -vvv -n $PARALLEL $pipeline_dir/iplLongitudinalPipeline.py \
  -L \
- -l $data_dir/nc_scan_rescan_validation_list.csv \
+ -l $data_dir/subject43.csv \
  -o $output_dir \
  --model-dir=$icbm_model_dir \
  --model-name=mni_icbm152_t1_tal_nlin_sym_09c  \

iplPatient.py

@@ -76,9 +76,6 @@ def __init__(self, id):
         self.run_skullreg = False  # default - do not attempt to run skull registration
         self.large_atrophy = False  # default - do not use the ventricle mask for the linear template creation
         self.geo_corr = False  # default - do not perform distortion correction
-        self.dohc = False  #  default - do not perform hippocampi segmentation
-        self.dovent = False  #  default - do not perform ventricle segmentation
-        self.doface = False  #  default - do not perform FACE cortical segmntation
         self.dodbm = False  #  default - do not perform ventricle segmentation
         self.vbm_options = {} # VBM options
 
@@ -620,13 +617,6 @@ def setFilenames(patient):
         patient[tp].vbm['ixfm']  = vbmdir + 'vbm_xfm_'    + patient.id + '_' + tp + '_inverse.xfm'
         patient[tp].vbm['igrid'] = vbmdir + 'vbm_xfm_'    + patient.id + '_' + tp + '_inverse_grid_0.mnc'
 
-        # FACE
-        patient[tp].face['basedir'] = facedir
-        patient[tp].face['Makefile'] = facedir + 'Makefile'
-        patient[tp].face['qc'] = facedir + os.sep + 'verify' + os.sep \
-            + 'verify_surfaces.jpg'
-        patient[tp].face['lobes'] = facedir + os.sep + 'atlas' + os.sep \
-            + 'lobes.csv'
 
         # TODO: add more needed files
         # end of timepoints