Changes to adapt the installation to the upcoming version 0.1.2 .

Author: Gab-D-G

Dockerfile

@@ -130,18 +130,18 @@ ENV export RABIES_VERSION=0.1.2 \
 
 RUN export RABIES_VERSION=0.1.2 && \
   export RABIES=$HOME/RABIES-${RABIES_VERSION} && \
-  #mkdir -p temp && \
-  #curl -L --retry 5 -o temp/RABIES.tar.gz https://github.com/CoBrALab/RABIES/archive/${RABIES_VERSION}.tar.gz && \
-  #cd temp && \
-  #tar zxf RABIES.tar.gz && \
-  #cd .. && \
-  #conda env create -f temp/RABIES-${RABIES_VERSION}/rabies_environment.yml && \
-  #bash temp/RABIES-${RABIES_VERSION}/install.sh && \
-  #rm -r temp && \
-  git clone https://github.com/CoBrALab/RABIES && \
-  mv RABIES $RABIES && \
-  conda env create -f $RABIES/rabies_environment.yml && \
-  bash $RABIES/install.sh && \
+  mkdir -p temp && \
+  curl -L --retry 5 -o temp/RABIES.tar.gz https://github.com/CoBrALab/RABIES/archive/${RABIES_VERSION}.tar.gz && \
+  cd temp && \
+  tar zxf RABIES.tar.gz && \
+  cd .. && \
+  conda env create -f temp/RABIES-${RABIES_VERSION}/rabies_environment.yml && \
+  bash temp/RABIES-${RABIES_VERSION}/install.sh && \
+  rm -r temp && \
+  #git clone https://github.com/CoBrALab/RABIES && \
+  #mv RABIES $RABIES && \
+  #conda env create -f $RABIES/rabies_environment.yml && \
+  #bash $RABIES/install.sh && \
   DSURQE_100micron_labels=${RABIES}/template_files/DSURQE_100micron_labels.nii.gz && \
   csv_labels=${RABIES}/template_files/DSURQE_40micron_R_mapping.csv && \
   /home/rabies/miniconda-latest/envs/rabies/bin/python ${RABIES}/gen_masks.py $DSURQE_100micron_labels $csv_labels ${RABIES}/template_files/DSURQE_100micron

README.md

@@ -88,7 +88,7 @@ cluster options for running ants_dbm (options copied from twolevel_dbm.py)::
   --local_threads LOCAL_THREADS
                         For local execution, how many subject-wise modelbuilds
                         to run in parallel, defaults to number of CPUs
-                        (default: 2)
+                        (default: 8)
   --template_reg_script TEMPLATE_REG_SCRIPT
                         Registration script that will be used for registration
                         of the generated template to the provided atlas for
@@ -111,33 +111,33 @@ Specify Slice Timing Correction info that is fed to AFNI 3dTshift.:
 Template files.:
   --anat_template ANAT_TEMPLATE
                         Anatomical file for the commonspace template.
-                        (default: /home/gabriel/RABIES-0.1.1/template_files/DS
-                        URQE_100micron_average.nii.gz)
+                        (default: /home/cic/desgab/RABIES-0.1.2/template_files
+                        /DSURQE_100micron_average.nii.gz)
   --brain_mask BRAIN_MASK
-                        Brain mask for the template. (default: /home/gabriel/R
-                        ABIES-0.1.1/template_files/DSURQE_100micron_mask.nii.g
-                        z)
-  --WM_mask WM_MASK     White matter mask for the template. (default: /home/ga
-                        briel/RABIES-0.1.1/template_files/DSURQE_100micron_ero
-                        ded_WM_mask.nii.gz)
-  --CSF_mask CSF_MASK   CSF mask for the template. (default: /home/gabriel/RAB
-                        IES-0.1.1/template_files/DSURQE_100micron_eroded_CSF_m
-                        ask.nii.gz)
+                        Brain mask for the template. (default: /home/cic/desga
+                        b/RABIES-0.1.2/template_files/DSURQE_100micron_mask.ni
+                        i.gz)
+  --WM_mask WM_MASK     White matter mask for the template. (default: /home/ci
+                        c/desgab/RABIES-0.1.2/template_files/DSURQE_100micron_
+                        eroded_WM_mask.nii.gz)
+  --CSF_mask CSF_MASK   CSF mask for the template. (default: /home/cic/desgab/
+                        RABIES-0.1.2/template_files/DSURQE_100micron_eroded_CS
+                        F_mask.nii.gz)
   --vascular_mask VASCULAR_MASK
                         Can provide a mask of major blood vessels for
                         computing confound timeseries. The default mask was
                         generated by applying MELODIC ICA and selecting the
                         resulting component mapping onto major veins.
                         (Grandjean et al. 2020, NeuroImage; Beckmann et al.
-                        2005) (default: /home/gabriel/RABIES-0.1.1/template_fi
-                        les/vascular_mask.nii.gz)
-  --labels LABELS       Atlas file with anatomical labels. (default: /home/gab
-                        riel/RABIES-0.1.1/template_files/DSURQE_100micron_labe
-                        ls.nii.gz)
+                        2005) (default: /home/cic/desgab/RABIES-0.1.2/template
+                        _files/vascular_mask.nii.gz)
+  --labels LABELS       Atlas file with anatomical labels. (default: /home/cic
+                        /desgab/RABIES-0.1.2/template_files/DSURQE_100micron_l
+                        abels.nii.gz)
 
 ```
 
-## Example execution command
+## Command syntax
 ```
   rabies nii_inputs/ rabies_outputs/ --bids_input -e -r light_SyN --template_reg_script light_SyN --TR 1.0s --cluster_type sge -p SGEGraph
 ```

install.sh

@@ -6,11 +6,11 @@ export RABIES=$HOME/RABIES-${RABIES_VERSION}
 export PYTHONPATH="${PYTHONPATH}:$RABIES"
 
 cd $HOME
-#curl -L --retry 5 -o $HOME/RABIES.tar.gz https://github.com/CoBrALab/RABIES/archive/${RABIES_VERSION}.tar.gz
-#tar zxf $HOME/RABIES.tar.gz
-#rm $HOME/RABIES.tar.gz
-git clone https://github.com/CoBrALab/RABIES
-mv RABIES $RABIES
+curl -L --retry 5 -o $HOME/RABIES.tar.gz https://github.com/CoBrALab/RABIES/archive/${RABIES_VERSION}.tar.gz
+tar zxf $HOME/RABIES.tar.gz
+rm $HOME/RABIES.tar.gz
+#git clone https://github.com/CoBrALab/RABIES
+#mv RABIES $RABIES
 
 #creates an executable script to execute rabies
 mkdir -p $RABIES/bin