Merge pull request #352 from a3sha2/master

task update
PennLINC · Jun 28, 2020 · 0672464 · 0672464
2 parents 3d217f1 + ecb3677
commit 0672464
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Showing 2 changed files with 20 additions and 9 deletions.
diff --git a/docs/flywheel.rst b/docs/flywheel.rst
@@ -15,7 +15,7 @@ as shown below.
 
 The cohort file will be created base on the FMRIPREP output and/or  img.  The `img` is input  directory for asl and structural image. The processing of ASL requires  
 processed anatomical image from FRMIPREP (fmriprepdir) or structural processing output (antsct). The  `m0` is the M0 directory for CBF calibration if present. In the case 
-of task-activation analysis, `task_name` is required to be specified in the config of xcpengine gear.
+of task-activation analysis, `task_name`  and `seission` are required to be specified in the config of xcpengine gear.
 
    Task-activation analysis
 -----------------------------

diff --git a/modules/task/task.mod b/modules/task/task.mod
@@ -224,6 +224,12 @@ if (( ${task_fmriprep[cxt]} == 1 ))
            maskpart2=${mask1#*_*_*_*}
         fi
         refpart="_boldref.nii.gz"; refvol=${imgprt2}${refpart}
+
+        conf2="_desc-confounds_regressors.json"
+        if [[ -f ${imgprt}${conf2} ]]; then 
+           exec_sys cp ${imgprt}${conf2} $out/prestats/${prefix}_fmriconf.json
+           output confjson $out/prestats/${prefix}_fmriconf.json
+        fi
 
        output fmriprepconf  ${out}/task/${prefix}_fmriconf.tsv 
        output    rps       ${out}/task/${prefix}_motion.1D
@@ -438,10 +444,14 @@ if (( ${task_fmriprep[cxt]} == 1 ))
                         oas2mni="  $(ls -d ${XCPEDIR}/space/OASIS/OASIS_transforms/OASIS-MNI_0Warp.nii.gz)
                           $(ls -d ${XCPEDIR}/space/OASIS/OASIS_transforms/OASIS-MNI_1Affine.mat)"
 
-                       mnitoas=$( echo ${mnitoas})
-                       oas2mni=$(echo ${oas2mni})
-                       mnitoas=${mnitoas// /,}
-                       oas2mni=${oas2mni// /,}
+                       mnitopnc=" $(ls -d ${XCPEDIR}/space/PNC/PNC_transforms/MNI-PNC_1Warp.nii.gz)
+                                    $(ls -d ${XCPEDIR}/space/PNC/PNC_transforms/MNI-PNC_0Affine.mat)"
+                       pnc2mni=" $(ls -d ${XCPEDIR}/space/PNC/PNC_transforms/PNC-MNI_0Warp.nii.gz)
+                                    $(ls -d ${XCPEDIR}/space/PNC/PNC_transforms/PNC-MNI_1Affine.mat)"
+                       mnitopnc=$( echo ${mnitopnc})
+                       pnc2mni=$(echo ${pnc2mni})
+                       mnitopnc=${mnitopnc// /,}
+                       pnc2mni=${pnc2mni// /,}
 
                        ${XCPEDIR}/utils/spaceMetadata  \
                          -o ${spaces[sub]}                 \
@@ -450,10 +460,6 @@ if (( ${task_fmriprep[cxt]} == 1 ))
                          -x ${oas2mni} -i ${mnitoas}     \
                          -s ${spaces[sub]} 2>/dev/null
 
-                       subj2temp="   $(ls -d ${antsct[sub]}/*SubjectToTemplate1Warp.nii.gz)
-                           $(ls -d ${antsct[sub]}/*SubjectToTemplate0GenericAffine.mat)"
-                     temp2subj="   $(ls -d ${antsct[sub]}/*TemplateToSubject0Warp.nii.gz) 
-                          $(ls -d ${antsct[sub]}/*TemplateToSubject1GenericAffine.mat)"
                        mnitopnc=$( echo ${mnitopnc})
                        pnc2mni=$(echo ${pnc2mni})
                        mnitopnc=${mnitopnc// /,}
@@ -760,8 +766,13 @@ done
     exec_xcp mbind.R -x    ${confmat[cxt]}  -y    OPdx${dx} -o    ${confmat_path}
     output   confmat           ${prefix}_confmat.1D
     ac_path=${outdir}/${prefix}_acompcor.1D
+    if [[ -f ${confjson[cxt]} ]]; then 
+     exec_xcp acompcor_select.py -j ${confjson[cxt]} -c ${fmriprepconf[cxt]} \
+    -o  ${ac_path} 
+    else
     exec_xcp generate_confmat.R -i ${fmriprepconf[cxt]} -j aCompCor  -o ${ac_path}
     output acp  ${prefix}_acompcor.1D
+    fi
     exec_xcp mbind.R  -x ${confmat[cxt]} -y ${acp[cxt]} -o ${confmat_path} 
     output confmat             ${prefix}_confmat.1D
    elif  [[ ${task_confound[cxt]} == acompcor_gsr ]] ; then