future 0.6

Author: davidmeunier79

docs/command.rst

@@ -31,7 +31,7 @@ For container (docker and singularity), here are some examples - add your proper
 
 .. code:: bash
 
-    $ singularity run -v binding_to_host:binding_guest /path/to/containers/macapype_v0.0.4.1.sif segment_pnh
+    $ singularity run -v binding_to_host:binding_guest /path/to/containers/macapype_v0.6.sif segment_pnh
 
 Expected input data
 *******************

docs/docker_install.rst

@@ -36,7 +36,7 @@ Starting from the release v0.2.1 on github, the docker images are tagged accordi
 
 .. code:: bash
 
-    $ docker pull macatools/macapype:version-0.2.1
+    $ docker pull macatools/macapype:v0.6
 
 
 See :ref:`Quick test <quick_test>` for testing if your docker installation works properly on test datasets.
@@ -50,7 +50,7 @@ Here is an example of a command line to install and convert the docker image to
 
 .. code:: bash
 
-    $ export SINGULARITY_TMPDIR=/tmp/; export SINGULARITY_CACHEDIR=/tmp/; sudo -E /path/to/bin/singularity build /path/to/containers/macapype_v0.4.2.sif docker://macatools/macapype:v0.4.2
+    $ export SINGULARITY_TMPDIR=/tmp/; export SINGULARITY_CACHEDIR=/tmp/; sudo -E /path/to/bin/singularity build /path/to/containers/macapype_v0.6.sif docker://macatools/macapype:v0.6
 
 It *seems* the sudo priviliges are required to install and build images, so in case you have trouble, ask the admin of your cluster to perform this operation
 

docs/quick_test.rst

@@ -25,13 +25,13 @@ Testing from Singularity image
 
 .. code:: bash
 
-    $ singularity run -B /path/to/data:/data /path/to/containers/macapype_v0.5.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_marmo -out /data/macapype_CI_v2.1/cerimed_marmo/results -soft ANTS_robustreg_test -species marmo -sub Tresor -ses 01 -deriv -padback -dt T1 T2
+    $ singularity run -B /path/to/data:/data /path/to/containers/macapype_v0.6.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_marmo -out /data/macapype_CI_v2.1/cerimed_marmo/results -soft ANTS_robustreg_test -species marmo -sub Tresor -ses 01 -deriv -padback -dt T1 T2
 
-    $ singularity run -B /path/to/data:/data /path/to/containers/macapype_v0.5.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_marmo -out /data/macapype_CI_v2.1/cerimed_marmo/results -soft ANTS_robustreg_prep -species marmo -sub Tresor -ses 01 -deriv -padback -dt T1 T2
+    $ singularity run -B /path/to/data:/data /path/to/containers/macapype_v0.6.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_marmo -out /data/macapype_CI_v2.1/cerimed_marmo/results -soft ANTS_robustreg_prep -species marmo -sub Tresor -ses 01 -deriv -padback -dt T1 T2
 
-    $ singularity run -B /path/to/data:/data /path/to/containers/macapype_v0.5.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_marmo -out /data/macapype_CI_v2.1/cerimed_marmo/results -soft ANTS_robustreg_noseg -species marmo -sub Tresor -ses 01 -deriv -padback -dt T1 T2
+    $ singularity run -B /path/to/data:/data /path/to/containers/macapype_v0.6.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_marmo -out /data/macapype_CI_v2.1/cerimed_marmo/results -soft ANTS_robustreg_noseg -species marmo -sub Tresor -ses 01 -deriv -padback -dt T1 T2
 
-    $ singularity run -B /path/to/data:/data /path/to/containers/macapype_v0.5.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_marmo -out /data/macapype_CI_v2.1/cerimed_marmo/results -soft ANTS_robustreg -species marmo -sub Tresor -ses 01 -deriv -padback -dt T1 T2
+    $ singularity run -B /path/to/data:/data /path/to/containers/macapype_v0.6.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_marmo -out /data/macapype_CI_v2.1/cerimed_marmo/results -soft ANTS_robustreg -species marmo -sub Tresor -ses 01 -deriv -padback -dt T1 T2
 
 
 The 4 commands earlier corresponds to brain segmentation performed on an example of marmoset (Tresor) . The 4 steps corresponds to incremental processings, and can performed in the given order. It is possible to test directly the last command (with *-soft ANTS*), but the caching system of nipype should work and the previous steps will not be performed again.
@@ -64,11 +64,11 @@ The 4 commands earlier corresponds to brain segmentation performed on an example
 Testing from docker image
 ------------------------
 
-For testing the docker installation, the beginning of the commands should be replaced by docker run -v /path/to/data:/data macatools/macapype:v0.3.1, e.g.
+For testing the docker installation, the beginning of the commands should be replaced by docker run -v /path/to/data:/data macatools/macapype:v0.6, e.g.
 
 .. code:: bash
 
-    $ docker run -v /path/to/data:/data macatools/macapype:v0.5 segment_pnh -data /data/macapype_CI_v2.1/cerimed_marmo -out /data/macapype_CI_v2.1/cerimed_marmo/results -soft ANTS_robustreg -species marmo -sub Tresor -ses 01 -deriv -padback -dt T1 T2
+    $ docker run -v /path/to/data:/data macatools/macapype:v0.6 segment_pnh -data /data/macapype_CI_v2.1/cerimed_marmo -out /data/macapype_CI_v2.1/cerimed_marmo/results -soft ANTS_robustreg -species marmo -sub Tresor -ses 01 -deriv -padback -dt T1 T2
 
 
 Testing from python package install
@@ -100,22 +100,22 @@ Baboon
 
 .. code:: bash
 
-    $ singularity run -B /path/to/data/:/data /path/to/containers/macapype_v0.5.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_baboon -out /data/macapype_CI_v2.1/cerimed_baboon/results_adult -soft ANTS -species baboon -sub Prune -ses 3 -deriv -padback -dt T1 T2  -indiv /data/cerimed_baboon/indiv_params_segment_baboon.json
+    $ singularity run -B /path/to/data/:/data /path/to/containers/macapype_v0.6.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_baboon -out /data/macapype_CI_v2.1/cerimed_baboon/results_adult -soft ANTS -species baboon -sub Prune -ses 3 -deriv -padback -dt T1 T2  -indiv /data/cerimed_baboon/indiv_params_segment_baboon.json
 
-    $ singularity run -B /path/to/data/:/data /path/to/containers/macapype_v0.5.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_baboon -out /data/macapype_CI_v2.1/cerimed_baboon/results_all_ages -soft ANTS -species baboon3 -sub Prune -ses 3 -deriv -padback -dt T1 T2  -indiv /data/cerimed_baboon/indiv_params_segment_baboon.json
+    $ singularity run -B /path/to/data/:/data /path/to/containers/macapype_v0.6.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_baboon -out /data/macapype_CI_v2.1/cerimed_baboon/results_all_ages -soft ANTS -species baboon3 -sub Prune -ses 3 -deriv -padback -dt T1 T2  -indiv /data/cerimed_baboon/indiv_params_segment_baboon.json
 
-    $ singularity run -B /path/to/data/:/data /path/to/containers/macapype_v0.5.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_baboon -out /data/macapype_CI_v2.1/cerimed_baboon/results_all_ages -soft ANTS -species baboon2 -sub Prune -ses 2 -deriv -padback -dt T1 T2  -indiv /data/cerimed_baboon/indiv_params_segment_baboon.json
+    $ singularity run -B /path/to/data/:/data /path/to/containers/macapype_v0.6.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_baboon -out /data/macapype_CI_v2.1/cerimed_baboon/results_all_ages -soft ANTS -species baboon2 -sub Prune -ses 2 -deriv -padback -dt T1 T2  -indiv /data/cerimed_baboon/indiv_params_segment_baboon.json
 
-    $ singularity run -B /path/to/data/:/data /path/to/containers/macapype_v0.5.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_baboon -out /data/macapype_CI_v2.1/cerimed_baboon/results_all_ages -soft ANTS -species baboon1 -sub Prune -ses 1 -deriv -padback -dt T1 T2  -indiv /data/cerimed_baboon/indiv_params_segment_baboon.json
+    $ singularity run -B /path/to/data/:/data /path/to/containers/macapype_v0.6.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_baboon -out /data/macapype_CI_v2.1/cerimed_baboon/results_all_ages -soft ANTS -species baboon1 -sub Prune -ses 1 -deriv -padback -dt T1 T2  -indiv /data/cerimed_baboon/indiv_params_segment_baboon.json
 
-    $ singularity run -B /path/to/data/:/data /path/to/containers/macapype_v0.5.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_baboon -out /data/macapype_CI_v2.1/cerimed_baboon/results_all_ages -soft ANTS -species baboon0 -sub Prune -ses 0 -deriv -padback -dt T1 T2  -indiv /data/cerimed_baboon/indiv_params_segment_baboon.json
+    $ singularity run -B /path/to/data/:/data /path/to/containers/macapype_v0.6.sif segment_pnh -data /data/macapype_CI_v2.1/cerimed_baboon -out /data/macapype_CI_v2.1/cerimed_baboon/results_all_ages -soft ANTS -species baboon0 -sub Prune -ses 0 -deriv -padback -dt T1 T2  -indiv /data/cerimed_baboon/indiv_params_segment_baboon.json
 
 Macaque
 *******
 
 .. code:: bash
 
-    $ singularity run -B /path/to/data/:/data /path/to/containers/macapype_v0.5.sif segment_pnh -data segment_pnh -data /data/macapype_CI_v2.1/cerimed_macaque -out /data/macapype_CI_v2.1/cerimed_macaque/results -soft ANTS_robustreg -sub Stevie -ses 01 -deriv -padback -dt T1 T2 -species macaque
+    $ singularity run -B /path/to/data/:/data /path/to/containers/macapype_v0.6.sif segment_pnh -data segment_pnh -data /data/macapype_CI_v2.1/cerimed_macaque -out /data/macapype_CI_v2.1/cerimed_macaque/results -soft ANTS_robustreg -sub Stevie -ses 01 -deriv -padback -dt T1 T2 -species macaque
 
 Testing different pipelines and options
 #######################################

macapype/_version.py

@@ -1 +1 @@
-__version__ = '0.6-rc3'
+__version__ = '0.6-rc4'