padback

Author: davidmeunier79

docs/command.rst

@@ -104,7 +104,7 @@ optional parameters
 
 * ``-deriv`` : creates a derivatives directory, with all important files, properly named following BIDS derivatives convertion. See :ref:`Derivatives <derivatives>` for a descrition of the outputs
 
-* ``-pad`` : exports most important files in native (original) space
+* ``-padback`` : exports most important files in native (original) space
 
 ------------------------
 more optional parameters
@@ -135,4 +135,4 @@ Command line examples
 
 .. code:: bash
 
-    $ python workflows/segment_pnh.py -data ~/Data_maca -out ./local_test -soft ANTS -params params.json -sub Apache Baron -ses 01 -rec mean -deriv -pad
+    $ python workflows/segment_pnh.py -data ~/Data_maca -out ./local_test -soft ANTS -params params.json -sub Apache Baron -ses 01 -rec mean -deriv -padback

docs/derivatives.rst

@@ -13,11 +13,13 @@ Depending on the options provided by command line and params.json, different fil
 
 Derivatives will be output if option ``-deriv`` is provided to the command line (See `Commands <commands>`):
 
-All files are by default in stereo space; if option ``-pad`` is provided to the command line (See `Commands <commands>`), files in native  will also be output.
+All files are by default in stereo space; if option ``-padback`` is provided to the command line (See `Commands <commands>`), files in native  will also be output.
 
 Data Preparation
 ****************
 
+|
+
 Original files (possibly after reorientation and avereging):
 
 *sub-Stevie_ses-01_space-native_T1w.nii.gz*
@@ -26,7 +28,7 @@ Original files (possibly after reorientation and avereging):
 
 |
 
-If -pad is defined in command line (See `Commands <commands>`):
+If ``-padback`` is defined in command line (See `Commands <commands>`):
 
 *sub-Stevie_ses-01_space-native_desc-denoised_T1w.nii.gz*
 
@@ -68,18 +70,26 @@ Transformations:
 
 *sub-Stevie_ses-01_space-stereo_target-native_affine.txt*
 
+|
+
 Brain extraction
 ****************
 
+|
+
 Brain mask:
 
 *sub-Stevie_ses-01_space-stereo_desc-brain_mask.nii.gz*
 
 *sub-Stevie_ses-01_space-native_desc-brain_mask.nii.gz*
 
+|
+
 Brain segmentation
 ******************
 
+|
+
 Brainmasked files after T1*T2 Bias correction:
 
 *sub-Stevie_ses-01_space-stereo_desc-debiased_desc-brain_T1w.nii.gz*
@@ -114,9 +124,13 @@ Segmentated files as indexed tisses:
 
 *sub-Stevie_ses-01_space-native_desc-brain_dseg.nii.gz*
 
+|
+
 Optional Post brain segmentation
 ********************************
 
+|
+
 Segmented files in mrtrix format:
 
 *sub-Stevie_ses-01_space-stereo_desc-5tt_dseg.nii.gz*

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 -pad -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_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 -pad -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_v0.5.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 -pad -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_v0.5.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 -pad -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
 
 
 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.
@@ -68,7 +68,7 @@ For testing the docker installation, the beginning of the commands should be rep
 
 .. 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 -pad -dt T1 T2
+    $ 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
 
 
 Testing from python package install
@@ -78,13 +78,13 @@ From pip install
 ~~~~~~~~~~~~~~~~
 .. code:: bash
 
-    $ segment_pnh -data /path/to/data/macapype_CI_v2.1/cerimed_marmo -out /path/to/data/macapype_CI_v2.1/cerimed_marmo/results -soft ANTS_robustreg -species marmo -sub Tresor -ses 01 -deriv -pad -dt T1 T2
+    $ segment_pnh -data /path/to/data/macapype_CI_v2.1/cerimed_marmo -out /path/to/data/macapype_CI_v2.1/cerimed_marmo/results -soft ANTS_robustreg -species marmo -sub Tresor -ses 01 -deriv -padback -dt T1 T2
 
 From github install
 ~~~~~~~~~~~~~~~~
 .. code:: bash
 
-    $ python workflows/segment_pnh.py -data /path/to/data/macapype_CI_v2.1/cerimed_marmo -out /path/to/data/macapype_CI_v2.1/cerimed_marmo/results -soft ANTS_robustreg -species marmo -sub Tresor -ses 01 -deriv -pad -dt T1 T2
+    $ python workflows/segment_pnh.py -data /path/to/data/macapype_CI_v2.1/cerimed_marmo -out /path/to/data/macapype_CI_v2.1/cerimed_marmo/results -soft ANTS_robustreg -species marmo -sub Tresor -ses 01 -deriv -padback -dt T1 T2
 
 **Note the /path/to/data instead of /data (as in the container install) in the arguments**
 
@@ -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 -pad -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_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 -pad -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_v0.5.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 -pad -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_v0.5.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 -pad -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_v0.5.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 -pad -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
 
 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 -pad -dt T1 T2 -species macaque
+    $ 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
 
 Testing different pipelines and options
 #######################################

workflows/segment_pnh.py

@@ -624,7 +624,7 @@ def main():
                         help="output derivatives in BIDS orig directory",
                         required=False)
 
-    parser.add_argument("-pad", dest="pad", action='store_true',
+    parser.add_argument("-pad", "-padback", dest="pad", action='store_true',
                         help="padding mask and seg_mask",
                         required=False)