Merge pull request #113 from coalsont/msmall_mrfix

modify msmall scripts to support MR FIX data
Washington-University · May 19, 2019 · 1f89abc · 1f89abc
2 parents a81844e + 1483c84
commit 1f89abc
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Showing 5 changed files with 256 additions and 221 deletions.
diff --git a/Examples/Scripts/MSMAllPipelineBatch.sh b/Examples/Scripts/MSMAllPipelineBatch.sh
@@ -75,8 +75,24 @@ PRINTCOM=""
 
 ######################################### DO WORK ##########################################
 
+# fMRINames is for single-run FIX data, set MR FIX settings to empty
 fMRINames="rfMRI_REST1_LR@rfMRI_REST1_RL@rfMRI_REST2_LR@rfMRI_REST2_RL"
+mrfixNames=""
+mrfixConcatName=""
+mrfixNamesToUse=""
 OutfMRIName="rfMRI_REST"
+
+# For MR FIX, set fMRINames to empty
+#fMRINames=""
+# the original MR FIX parameter for what to concatenate
+#mrfixNames="rfMRI_REST1_RL@rfMRI_REST1_LR@tfMRI_WM_RL@tfMRI_WM_LR@tfMRI_GAMBLING_RL@tfMRI_GAMBLING_LR@tfMRI_MOTOR_RL@tfMRI_MOTOR_LR@rfMRI_REST2_LR@rfMRI_REST2_RL@tfMRI_LANGUAGE_RL@tfMRI_LANGUAGE_LR@tfMRI_SOCIAL_RL@tfMRI_SOCIAL_LR@tfMRI_RELATIONAL_RL@tfMRI_RELATIONAL_LR@tfMRI_EMOTION_RL@tfMRI_EMOTION_LR"
+# the original MR FIX concatenated name
+#mrfixConcatName="fMRI_CONCAT"
+# @-separate list of runs to use
+#mrfixNamesToUse="rfMRI_REST1_RL@rfMRI_REST1_LR@rfMRI_REST2_LR@rfMRI_REST2_RL"
+#OutfMRIName="rfMRI_REST_CONCAT"
+
+
 HighPass="2000"
 fMRIProcSTRING="_Atlas_hp2000_clean"
 MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll"
@@ -89,29 +105,32 @@ MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab
 fMRINames=`echo ${fMRINames} | sed 's/ /@/g'`
 
 for Subject in $Subjlist ; do
-	echo "    ${Subject}"
-
-	if [ -n "${command_line_specified_run_local}" ] ; then
-	    echo "About to run ${HCPPIPEDIR}/MSMAll/MSMAllPipeline.sh"
-	    queuing_command=""
-	else
-	    echo "About to use fsl_sub to queue or run ${HCPPIPEDIR}/MSMAll/MSMAllPipeline.sh"
-	    queuing_command="${FSLDIR}/bin/fsl_sub ${QUEUE}"
-	fi
-
-	${queuing_command} ${HCPPIPEDIR}/MSMAll/MSMAllPipeline.sh \
-  --path=${StudyFolder} \
-  --subject=${Subject} \
-  --fmri-names-list=${fMRINames} \
-  --output-fmri-name=${OutfMRIName} \
-  --high-pass=${HighPass} \
-  --fmri-proc-string=${fMRIProcSTRING} \
-  --msm-all-templates=${MSMAllTemplates} \
-  --output-registration-name=${RegName} \
-  --high-res-mesh=${HighResMesh} \
-  --low-res-mesh=${LowResMesh} \
-  --input-registration-name=${InRegName} \
-  --matlab-run-mode=${MatlabMode}
+    echo "    ${Subject}"
+
+    if [ -n "${command_line_specified_run_local}" ] ; then
+        echo "About to run ${HCPPIPEDIR}/MSMAll/MSMAllPipeline.sh"
+        queuing_command=""
+    else
+        echo "About to use fsl_sub to queue or run ${HCPPIPEDIR}/MSMAll/MSMAllPipeline.sh"
+        queuing_command="${FSLDIR}/bin/fsl_sub ${QUEUE}"
+    fi
+
+    ${queuing_command} ${HCPPIPEDIR}/MSMAll/MSMAllPipeline.sh \
+        --path=${StudyFolder} \
+        --subject=${Subject} \
+        --fmri-names-list=${fMRINames} \
+        --multirun-fix-names="${mrfixNames}" \
+        --multirun-fix-concat-name="${mrfixConcatName}" \
+        --multirun-fix-names-to-use="${mrfixNamesToUse}" \
+        --output-fmri-name=${OutfMRIName} \
+        --high-pass=${HighPass} \
+        --fmri-proc-string=${fMRIProcSTRING} \
+        --msm-all-templates=${MSMAllTemplates} \
+        --output-registration-name=${RegName} \
+        --high-res-mesh=${HighResMesh} \
+        --low-res-mesh=${LowResMesh} \
+        --input-registration-name=${InRegName} \
+        --matlab-run-mode=${MatlabMode}
 done