Add MSMSulc support

Author: kjamison

Dockerfile

@@ -134,12 +134,13 @@ RUN apt-get -y update \
 ENV HCPPIPEDIR=/opt/HCP-Pipelines
 
 #############################################
-# Install MSM binaries (from local directory)
-ENV MSMBin=${HCPPIPEDIR}/MSMBinaries
+# Download amnd install MSM_HOCR v3 binary
+ENV MSMBINDIR=${HCPPIPEDIR}/MSMBinaries
+
+RUN mkdir -p ${MSMBINDIR} && \
+    wget -nv https://github.com/ecr05/MSM_HOCR_macOSX/releases/download/1.0/msm_ubuntu14.04 -O ${MSMBINDIR}/msm && \
+    chmod +x ${MSMBINDIR}/msm
 
-# Copy MSM_HOCR_v2 binary
-# Skip this for now pending license questions
-#COPY MSM/Centos/msm ${MSMBin}/msm
 #############################################
 
 # Make directory for flywheel spec (v0)

README.md

@@ -22,6 +22,13 @@
     * If needed, this file can be obtained from the console at <code>C:\MedCom\MriSiteData\GradientCoil\coeff.grad</code> for Siemens scanners
     * Note: This effect is significant for HCP data collected on custom Siemens "ConnectomS" scanner, and for 7T scanners.  It is relatively minor for production 3T scanners (Siemens Trio, Prisma, etc.)
 
+## Configuration options
+1. Subject: Subject ID to use for outputs
+2. RegName: Surface registration type: either 'FS' (freesurfer) or 'MSMSulc' (HCP default). (See [FSL MSM](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MSM) for details on MSMSulc)
+3. BrainSize: Brain size in mm (in Superior-Inferior axis), typically 150 (default) for adults
+4. TemplateSize: Voxel size of HCP anatomical template. Best if matches input. (Options = 0.7mm, 0.8mm (default), 1mm)
+5. StructuralUnwarpDirection: Readout direction for structural scans ( 'x', 'x-', 'y', 'y-', 'z', 'z-' ). HCP default = 'z' (**Only used when providing fieldmaps to correct readout distortion**)
+
 ## Outputs
 * <code>\<subject\>\_hcpstruct.zip</code>: Zipped output directory containing complete <code>MNINonLinear/</code>, <code>T1w/</code>, and <code>T2w/</code> folders.
 * <code>\<subject\>\_hcpstruct\_QC.*.png</code>: QC images for visual inspection of output quality (details to come...)

manifest.json

@@ -87,6 +87,11 @@
       "default": "000000",
       "description": "Subject ID (Default = 000000)"
     },
+    "RegName": {
+      "type": "string",
+      "default": "MSMSulc",
+      "description": "Surface registration type: either 'FS' (freesurfer) or 'MSMSulc' (HCP default)"
+    },
     "BrainSize": {
       "type": "integer",
       "default": 150,

run

@@ -59,6 +59,7 @@ mkdir -p ${LogFileDirFull}
 FSLSUBOPTIONS="-l ${LogFileDirFull}"
 
 #Default Config Settings
+RegName="FS"
 StructuralUnwarpDir="z" #z appears to be best or "NONE" if not used
 StructuralDeltaTE="NONE" #DeltaTE for GRE fieldmap used to correct STRUCTURAL
 StructuralDwellTime="NONE" # DwellTime for SpinEchoFieldMap when TOPUP is used for STRUCTURAL (ie: not T1wSampleSpacing)
@@ -182,13 +183,22 @@ fi
 
 # Install FreeSurfer license
 if [[ -e "${FW_INPUT_FreeSurferLicense}" ]]; then
-  echo -e "$CONTAINER Copying user-supplied FreeSurfer license file to ${FREESURFER_HOME}/license.txt"
+  echo -e "$CONTAINER [$(timestamp)] Copying user-supplied FreeSurfer license file to ${FREESURFER_HOME}/license.txt"
   cp -f "${FW_INPUT_FreeSurferLicense}" ${FREESURFER_HOME}/license.txt
 fi
 
+# Check RegName config
+case $(toupper "${FW_CONFIG_RegName}") in
+  FS|MSMSULC)
+    RegName="${FW_CONFIG_RegName}"
+    ;;
+  *)
+    echo -e "$CONTAINER [$(timestamp)] RegName must be FS or MSMSulc!"
+    exit 1
+    ;;
+esac
+
 Subject=${FW_CONFIG_Subject}
-RegName="FS" #Only allow FreeSurfer surface registration pending MSM license questions
-#RegName=${FW_CONFIG_RegName}
 BrainSize=${FW_CONFIG_BrainSize}
 TemplateSize=${FW_CONFIG_TemplateSize}
 UnwarpDir=${FW_CONFIG_StructuralUnwarpDirection}
@@ -399,10 +409,10 @@ fi
 #    new element called ".config" so the new file can be read as though it was flywheel config.json
 OUTPUT_CONFIG_FILE=${StudyFolder}/${Subject}/${Subject}_hcpstruct_config.json
 jq -r '.config.RegName = "'"${RegName}"'" | .config.Subject = "'"${Subject}"'" | .config | {config: .}' $CONFIG_FILE \
-  | jq -r '.config.FinalfMRIResolution = "'"${FinalfMRIResolution}"'"' \
   | jq -r '.config.GrayordinatesResolution = "'"${GrayordinatesResolution}"'"' \
-  | jq -r '.config.LowResMesh = "'"${LowResMesh}"'"' \
-  | jq -r '.config.SmoothingFWHM = "'"${SmoothingFWHM}"'"' > ${OUTPUT_CONFIG_FILE}
+  | jq -r '.config.GrayordinatesTemplate = "'"${GrayordinatesTemplate}"'"' \
+  | jq -r '.config.HighResMesh = "'"${HighResMesh}"'"' \
+  | jq -r '.config.LowResMesh = "'"${LowResMesh}"'"' > ${OUTPUT_CONFIG_FILE}
 
 # If pipeline successful, zip outputs and clean up
 outputzipname=${Subject}_hcpstruct.zip 

scripts/bash_functions.sh

@@ -1,4 +1,6 @@
 #needed to clean up some of the numerical config options (if empty or non-numerical, output empty)
-print_decimal_number () { echo $1 | awk '{if($1*1 == $1) printf "%.15f\n", $1; else print ""}'; };
-
+#optional second input = number of decimal places (Default = 15)
+print_decimal_number () { dec=$(echo $2 15 | awk '{print $1}'); echo $1 | awk '{if($1*1 == $1) printf "%.'${dec}'f\n", $1; else print ""}'; };
 timestamp () { date +"%Y-%m-%d %H:%M:%S %Z"; }
+toupper() { echo "$@" | tr '[:lower:]' '[:upper:]'; };
+tolower() { echo "$@" | tr '[:upper:]' '[:lower:]'; };