Merge pull request #36 from BIDS-Apps/enh/6.0.1

Update to version 6.0.1

Dockerfile

@@ -2,7 +2,7 @@ FROM ubuntu:trusty
 
 RUN apt-get update \
     && apt-get install -y wget
-RUN wget -qO- https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar zxv -C /opt \
+RUN wget -qO- https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt \
     --exclude='freesurfer/trctrain' \
     --exclude='freesurfer/subjects/fsaverage_sym' \
     --exclude='freesurfer/subjects/fsaverage3' \
@@ -60,7 +60,6 @@ ENV PERL5LIB /opt/freesurfer/mni/lib/perl5/5.8.5
 ENV MNI_PERL5LIB /opt/freesurfer/mni/lib/perl5/5.8.5
 ENV PATH /opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
 ENV PYTHONPATH=""
-RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
 
 RUN mkdir /scratch
 RUN mkdir /local-scratch

README.md

@@ -71,10 +71,9 @@ This App has the following command line arguments:
           --template_name TEMPLATE_NAME
                                 Name for the custom group level template generated for
                                 this dataset
-          --license_key LICENSE_KEY
-                                FreeSurfer license key - letters and numbers after "*"
-                                in the email you received after registration. To
-                                register (for free) visit
+          --license_file LICENSE_FILE
+                                Path to FreeSurfer license key file. To obtain it you 
+								need to register (for free) visit
                                 https://surfer.nmr.mgh.harvard.edu/registration.html
           --acquisition_label ACQUISITION_LABEL
                                 If the dataset contains multiple T1 weighted images
@@ -112,7 +111,7 @@ To run it in participant level mode (for one participant):
 		-v /Users/filo/outputs:/outputs \
 		bids/freesurfer \
 		/bids_dataset /outputs participant --participant_label 01 \
-		--license_key "XXXXXXXX"
+		--license_file "license.txt"
 
 
 #### Group level
@@ -126,7 +125,7 @@ To create a study specific template run:
 		-v /Users/filo/outputs:/outputs \
 		bids/freesurfer \
 		/bids_dataset /outputs group1 \
-		--license_key "XXXXXXXX"
+		--license_file "license.txt"
 
 To export tables with aggregated measurements within regions of
 cortical parcellation and subcortical segementation run:
@@ -136,5 +135,5 @@ cortical parcellation and subcortical segementation run:
 		-v /Users/filo/outputs:/outputs \
 		bids/freesurfer \
 		/bids_dataset /outputs group2 \
-		--license_key "XXXXXXXX"
+		--license_file "license.txt"
 Also see *--parcellations* and *--measurements* arguments.

circle.yml

@@ -22,19 +22,20 @@ dependencies:
     - docker build -t bids/${CIRCLE_PROJECT_REPONAME} . :
         timeout: 21600
     - mkdir -p ~/docker; docker save "bids/${CIRCLE_PROJECT_REPONAME}" > ~/docker/image.tar
+    - echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IGxpY2Vuc2UudHh0Cg==" | base64 -d | sh
 
 test:
   override:
     # print version
-    - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset bids/${CIRCLE_PROJECT_REPONAME,,} --version
-    - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/outputs1:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --license_key="~/test.key" --stages autorecon1 && cat ${HOME}/outputs1/sub-01/scripts/recon-all.done :
+    - docker run -ti --rm --read-only -v $PWD/license.txt:/license.txt -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset bids/${CIRCLE_PROJECT_REPONAME,,} --version
+    - docker run -ti --rm --read-only -v $PWD/license.txt:/license.txt -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/outputs1:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --license_file=/license.txt --stages autorecon1 && cat ${HOME}/outputs1/sub-01/scripts/recon-all.done :
         timeout: 21600
-    - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/outputs2:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --steps cross-sectional --session_label test --license_key="~/test.key" --stages autorecon1 && cat ${HOME}/outputs2/sub-01_ses-test/scripts/recon-all.done :
+    - docker run -ti --rm --read-only -v $PWD/license.txt:/license.txt -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/outputs2:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --steps cross-sectional --session_label test --license_file=/license.txt --stages autorecon1 && cat ${HOME}/outputs2/sub-01_ses-test/scripts/recon-all.done :
         timeout: 21600
     # group2 tests
-    - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/data/ds114_test1_freesurfer_precomp_v6.0.0:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group2 --license_key="~/test.key"  && mkdir -p ${HOME}/outputs1/ && sudo mv ${HOME}/data/ds114_test1_freesurfer_precomp_v6.0.0/00_group* ${HOME}/outputs1/ && cat ${HOME}/outputs1/00_group2_stats_tables/lh.aparc.thickness.tsv :
+    - docker run -ti --rm --read-only -v $PWD/license.txt:/license.txt -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/data/ds114_test1_freesurfer_precomp_v6.0.0:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group2 --license_file=/license.txt  && mkdir -p ${HOME}/outputs1/ && sudo mv ${HOME}/data/ds114_test1_freesurfer_precomp_v6.0.0/00_group* ${HOME}/outputs1/ && cat ${HOME}/outputs1/00_group2_stats_tables/lh.aparc.thickness.tsv :
         timeout: 21600
-    - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/data/ds114_test2_freesurfer_precomp_v6.0.0:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group2 --license_key="~/test.key"  && mkdir -p ${HOME}/outputs2/ && sudo mv ${HOME}/data/ds114_test2_freesurfer_precomp_v6.0.0/00_group* ${HOME}/outputs2/ && cat ${HOME}/outputs2/00_group2_stats_tables/lh.aparc.thickness.tsv :
+    - docker run -ti --rm --read-only -v $PWD/license.txt:/license.txt -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test2:/bids_dataset -v ${HOME}/data/ds114_test2_freesurfer_precomp_v6.0.0:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group2 --license_file=/license.txt  && mkdir -p ${HOME}/outputs2/ && sudo mv ${HOME}/data/ds114_test2_freesurfer_precomp_v6.0.0/00_group* ${HOME}/outputs2/ && cat ${HOME}/outputs2/00_group2_stats_tables/lh.aparc.thickness.tsv :
         timeout: 21600
 
 deployment: