Merge branch 'master' into FIX_notebook_kernel

Author: miykael

Dockerfile

@@ -63,7 +63,7 @@ RUN apt-get update -qq \
 
 RUN sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT
 
-ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib"
+ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
 
 ENV FORCE_SPMMCR="1" \
     LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64" \
@@ -212,7 +212,7 @@ RUN echo '{ \
     \n    [ \
     \n      "env", \
     \n      { \
-    \n        "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib" \
+    \n        "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH" \
     \n      } \
     \n    ], \
     \n    [ \

Singularity

@@ -204,7 +204,7 @@ echo '{
 \n    [
 \n      "env",
 \n      {
-\n        "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib"
+\n        "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
 \n      }
 \n    ],
 \n    [
@@ -319,7 +319,7 @@ echo '{
 export LANG="en_US.UTF-8"
 export LC_ALL="en_US.UTF-8"
 export ND_ENTRYPOINT="/neurodocker/startup.sh"
-export LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib"
+export LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH"
 export FORCE_SPMMCR="1"
 export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64"
 export MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"

generate.sh

@@ -11,7 +11,7 @@ generate_docker() {
                      git-annex-standalone vim emacs-nox nano less ncdu \
                      tig git-annex-remote-rclone octave netbase \
            --add-to-entrypoint "source /etc/fsl/fsl.sh" \
-           --env LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib" \
+           --env LD_LIBRARY_PATH='/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH' \
            --spm12 version=r7219 \
            --user=neuro \
            --miniconda miniconda_version="4.3.31" \
@@ -49,7 +49,7 @@ generate_singularity() {
                      git-annex-standalone vim emacs-nox nano less ncdu \
                      tig git-annex-remote-rclone octave netbase \
            --add-to-entrypoint "source /etc/fsl/fsl.sh" \
-           --env LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib" \
+           --env LD_LIBRARY_PATH='/opt/miniconda-latest/envs/neuro/lib:$LD_LIBRARY_PATH' \
            --spm12 version=r7219 \
            --user=neuro \
            --miniconda miniconda_version="4.3.31" \

notebooks/handson_preprocessing.ipynb

@@ -733,7 +733,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "**<span style=\"color:red\">Important</span>**: As you can see above, we also specified a variable `desired_voxel_iso`. This is very important at this stage, otherwise `FLIRT` will transform your functional images to a resolution of the anatomical image, which will dramatically increase the file size (e.g. to 1-10GB per file). If you don't want to change the voxel resolution, use the `no_resample=True` value instead of `apply_isoxfm=desired_voxel_iso`."
+    "**<span style=\"color:red\">Important</span>**: As you can see above, we also specified a variable `desired_voxel_iso`. This is very important at this stage, otherwise `FLIRT` will transform your functional images to a resolution of the anatomical image, which will dramatically increase the file size (e.g. to 1-10GB per file). If you don't want to change the voxel resolution, use the additional parameter `no_resample=True`. Important, for this to work, you still need to define `apply_isoxfm`."
    ]
   },
   {