From 4ed8030c0d15dfd814d6ea0c358d5d9315c7b95d Mon Sep 17 00:00:00 2001 From: Anders Perrone Date: Thu, 9 May 2019 16:02:11 -0700 Subject: [PATCH 1/3] Update MCRROOT in SetupEnv.sh --- app/SetupEnv.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/SetupEnv.sh b/app/SetupEnv.sh index 20f94e6..ff24d67 100755 --- a/app/SetupEnv.sh +++ b/app/SetupEnv.sh @@ -38,7 +38,7 @@ export MSMBINDIR=/opt/msm/Ubuntu # Set up DCAN Environment Variables -export MCRROOT=/opt/mcr/v91 +export MCRROOT=/opt/matlab/v91 export DCANBOLDPROCDIR=/opt/dcan-tools/dcan_bold_proc export DCANBOLDPROCVER=DCANBOLDProc_v4.0.0 export EXECSUMDIR=/opt/dcan-tools/executivesummary From b4e736a958a26c507c72c89a103fcadb315b4e6f Mon Sep 17 00:00:00 2001 From: Anders Perrone Date: Thu, 9 May 2019 16:48:34 -0700 Subject: [PATCH 2/3] Revert "Update MCRROOT in SetupEnv.sh" --- app/SetupEnv.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/SetupEnv.sh b/app/SetupEnv.sh index ff24d67..20f94e6 100755 --- a/app/SetupEnv.sh +++ b/app/SetupEnv.sh @@ -38,7 +38,7 @@ export MSMBINDIR=/opt/msm/Ubuntu # Set up DCAN Environment Variables -export MCRROOT=/opt/matlab/v91 +export MCRROOT=/opt/mcr/v91 export DCANBOLDPROCDIR=/opt/dcan-tools/dcan_bold_proc export DCANBOLDPROCVER=DCANBOLDProc_v4.0.0 export EXECSUMDIR=/opt/dcan-tools/executivesummary From ad43552000fca1843ad939a4ed24b6dfc1e589bb Mon Sep 17 00:00:00 2001 From: Anders Perrone Date: Mon, 19 Aug 2019 16:02:58 -0700 Subject: [PATCH 3/3] add atlas to exec summ --- app/pipelines.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/app/pipelines.py b/app/pipelines.py index fe8d11c..5892f11 100644 --- a/app/pipelines.py +++ b/app/pipelines.py @@ -954,7 +954,8 @@ class ExecutiveSummary(Stage): spec = ' --unproc_root={unproc}' \ ' --deriv_root={path}' \ ' --subject_id={subject}' \ - ' --ex_summ_dir={summary_dir}' + ' --ex_summ_dir={summary_dir}' \ + ' --atlas={t1templatebrain}' def __init__(self, config): super(__class__, self).__init__(config)