From 5b66c7497b156142f1dcafffcffd72b19f4730dc Mon Sep 17 00:00:00 2001 From: Kathy Snider Date: Fri, 26 Jun 2020 07:53:17 -0700 Subject: [PATCH 1/8] Newer version of matlab needed for newer internal tools. --- SetupEnv.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/SetupEnv.sh b/SetupEnv.sh index 9804428..d8ddd0a 100755 --- a/SetupEnv.sh +++ b/SetupEnv.sh @@ -16,7 +16,6 @@ export FREESURFER_HOME=/opt/freesurfer # Set up specific environment variables for the HCP Pipeline export HCPPIPEDIR=/opt/pipeline -export SCRATCHDIR=/tmp export HCPPIPEDIR_Templates=${HCPPIPEDIR}/global/templates export HCPPIPEDIR_Config=${HCPPIPEDIR}/global/config @@ -35,7 +34,8 @@ export MSMBin=${HCPPIPEDIR}/MSMBinaries # Set up DCAN Environment Variables -export MCRROOT=/opt/mcr/v91 +export SCRATCHDIR=/tmp +export MCRROOT=/opt/mcr/v92 export DCANBOLDPROCDIR=/opt/dcan-tools/dcan_bold_proc export DCANBOLDPROCVER=DCANBOLDProc_v4.0.0 export EXECSUMDIR=/opt/dcan-tools/executivesummary From 0765037d48d5cc8727944bc4c5a4540c78d637b0 Mon Sep 17 00:00:00 2001 From: Kathy <37816304+kathy-snider@users.noreply.github.com> Date: Fri, 7 Aug 2020 08:07:43 -0700 Subject: [PATCH 2/8] Get latest internal tools --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 7749988..1271966 100755 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM dcanlabs/internal-tools:v1.0.0 +FROM dcanlabs/internal-tools:v1.0.1 RUN apt-get update && apt-get install -yq --no-install-recommends \ apt-utils \ From d60f8661daa784485b2a73d4606c225bbe8747ad Mon Sep 17 00:00:00 2001 From: Kathy <37816304+kathy-snider@users.noreply.github.com> Date: Tue, 25 Aug 2020 14:14:35 -0700 Subject: [PATCH 3/8] Get latest pipeline w new INFANT_MNI_T1_1mm_brain.nii.gz --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 1271966..5c8364e 100755 --- a/Dockerfile +++ b/Dockerfile @@ -18,7 +18,7 @@ RUN python3 -m pip install -r "/app/requirements.txt" # insert pipeline code ADD https://github.com/DCAN-Labs/dcan-infant-pipeline.git version.json -RUN git clone -b 'v0.0.5' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan-infant-pipeline.git /opt/pipeline +RUN git clone -b 'v0.0.6' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan-infant-pipeline.git /opt/pipeline # unless otherwise specified... From bec59898b0c71d537b5b77e99428fd3fd8d6d20c Mon Sep 17 00:00:00 2001 From: Kathy <37816304+kathy-snider@users.noreply.github.com> Date: Tue, 15 Sep 2020 12:04:04 -0700 Subject: [PATCH 4/8] Debug added to FMRIVolume --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 5c8364e..7653653 100755 --- a/Dockerfile +++ b/Dockerfile @@ -18,7 +18,7 @@ RUN python3 -m pip install -r "/app/requirements.txt" # insert pipeline code ADD https://github.com/DCAN-Labs/dcan-infant-pipeline.git version.json -RUN git clone -b 'v0.0.6' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan-infant-pipeline.git /opt/pipeline +RUN git clone -b 'v0.0.7' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan-infant-pipeline.git /opt/pipeline # unless otherwise specified... From 86a3d13fddcf16bd7ad79425a99a6f0650e7644c Mon Sep 17 00:00:00 2001 From: Kathy <37816304+kathy-snider@users.noreply.github.com> Date: Tue, 15 Sep 2020 15:37:23 -0700 Subject: [PATCH 5/8] Adjusting debug --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 7653653..dbc9f35 100755 --- a/Dockerfile +++ b/Dockerfile @@ -18,7 +18,7 @@ RUN python3 -m pip install -r "/app/requirements.txt" # insert pipeline code ADD https://github.com/DCAN-Labs/dcan-infant-pipeline.git version.json -RUN git clone -b 'v0.0.7' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan-infant-pipeline.git /opt/pipeline +RUN git clone -b 'v0.0.7b' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan-infant-pipeline.git /opt/pipeline # unless otherwise specified... From ccd2bfa363fdf5b610d2548180860188445e1114 Mon Sep 17 00:00:00 2001 From: Kathy <37816304+kathy-snider@users.noreply.github.com> Date: Wed, 16 Sep 2020 02:46:26 -0700 Subject: [PATCH 6/8] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index dbc9f35..f89421a 100755 --- a/Dockerfile +++ b/Dockerfile @@ -18,7 +18,7 @@ RUN python3 -m pip install -r "/app/requirements.txt" # insert pipeline code ADD https://github.com/DCAN-Labs/dcan-infant-pipeline.git version.json -RUN git clone -b 'v0.0.7b' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan-infant-pipeline.git /opt/pipeline +RUN git clone -b 'v0.0.7c' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan-infant-pipeline.git /opt/pipeline # unless otherwise specified... From 599e68e4f9bf9ac6478461065d42f8ab0e60f1c3 Mon Sep 17 00:00:00 2001 From: Kathy <37816304+kathy-snider@users.noreply.github.com> Date: Tue, 22 Sep 2020 15:46:13 -0700 Subject: [PATCH 7/8] Error out when we don't have T2w data. --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index f89421a..1bb45c7 100755 --- a/Dockerfile +++ b/Dockerfile @@ -18,7 +18,7 @@ RUN python3 -m pip install -r "/app/requirements.txt" # insert pipeline code ADD https://github.com/DCAN-Labs/dcan-infant-pipeline.git version.json -RUN git clone -b 'v0.0.7c' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan-infant-pipeline.git /opt/pipeline +RUN git clone -b 'v0.0.8' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan-infant-pipeline.git /opt/pipeline # unless otherwise specified... From 3eb6a5bf43bd6ca6bba319393fc20617f7cba6d9 Mon Sep 17 00:00:00 2001 From: Kathy Snider Date: Mon, 26 Oct 2020 08:42:35 -0700 Subject: [PATCH 8/8] files/MNINonLinear/xfms/acpc_dc2standar is needed! --- baby_BIDS_cleaning.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/baby_BIDS_cleaning.json b/baby_BIDS_cleaning.json index 771d36a..62fedb3 100755 --- a/baby_BIDS_cleaning.json +++ b/baby_BIDS_cleaning.json @@ -2651,7 +2651,7 @@ "name": "acpc_dc2standard.nii.gz", "rel_path": "MNINonLinear/xfms/acpc_dc2standard.nii.gz", "size": 0, - "state": "delete", + "state": "keep", "type": "file" }, "e-2.nii.gz": {