Added FileMapper as a stage in the pipeline. (#20)

* Stage needs entry in table.

* Files needed to run filemapper for the infant pipeline.

* Tell the pipeline how to find the FileMapper files.

* Match filename to the file's name.

* Left out space between args.

* The pipeline uses the path to files; wrapper must 'find' root.

* Use env var to find filemapper script.

* Jsons need executable?

* Fix applicaton name.

* Correct the name of the script.

* Seem to have lost a bunch of my script.

* Seem to have lost a bunch of my script.

* Have tested and merged internal tools; can used tagged version now.

BIDS_filemapper_wrapper.sh

@@ -0,0 +1,149 @@
+#! /bin/bash
+
+# The file mapper uses a 'template' json file and replaces {SUBJECT}, {SESSION}, and
+# {PIPELINE} strings with the subject number, session number, and pipeline name provided
+# to it. However, it does not handle task-specific files (esp. motion regressors). This
+# wrapper looks for task-specific files for each of the tasks it finds in the pipeline's
+# output. It copies the task files to the appropriate locations/names and then calls
+# file_mapper_script.py to copy the non-task files.
+#
+
+# Required
+SUB=$1            # subject number - no 'sub-'.
+SES=$2            # session number - no 'ses-'.
+FILES=$3          # path to subject/session/files.
+TEMPLATE_JSON=$4  # json file to use as a template.
+shift 4
+
+PIPE=infant-abcd-bids-pipeline
+
+if [ -z "${SUB}" ] || [ -z "${SES}" ]  || [ -z "${FILES}" ]  || [ -z "${TEMPLATE_JSON}" ] ; then
+    echo "usage: $0 subject-id session-id path-to-processed-data path-to-template-json "
+    exit 1
+fi
+
+# Set up strings to use for subject, session, paths etc.
+session_dir=$( dirname ${FILES} )
+session=$( basename ${session_dir} )
+subject_dir=$( dirname ${session_dir} )
+subject=$(basename ${subject_dir} )
+if [[ "${session}" == "ses-${SES}" ]] && [[ "${subject}" == "sub-${SUB}" ]] ; then
+    ROOT=$( dirname ${subject_dir} )
+else
+    echo There is a problem with the processed data. Expected path to end with sub-${SUB}/ses-${SES}/files.
+    echo The path provided does not match that pattern. Path is: ${FILES}.
+fi
+
+results=${FILES}/MNINonLinear/Results
+if ! [ -d ${results} ]; then
+    echo "ERROR: Filemapper is unable to find directory ${results}. "
+    exit 1
+fi
+
+derivs="${ROOT}/derivatives/${PIPE}/${subject}/${session}"
+func="${derivs}/func"
+mkdir -p ${func}
+
+
+####### START PROCESSING #############
+# Handle special cases.
+#
+# Each subject/session can have a different set of tasks and different numbers
+# of runs of each.
+#
+# Furthermore, we may or may not have filtered files.
+#
+# These special cases cannot be handled with the json, because we would need
+# to put in source and destination files for every possible combination.
+
+shopt -s nullglob
+pushd ${results} > /dev/null
+
+# Each fMRI (task/run combination) has a subdirectory in processed files, in
+# MNINonLinear/Results. We can use those subdirectories to get the names of the
+# fMRIs.
+# If filtering (bandstop) was used, there will be one file of filtered movement
+# regressors for each fMRI.
+# For example:
+#    MNINonLinear/Results/ses-1_task-rest_run-02/DCANBOLDProc_v4.0.0/DCANBOLDProc_v4.0.0_bs18.582_25.7263_filtered_Movement_Regressors.txt
+
+filtered=( */DCANBOLDProc_v4.0.0/DCANBOLDProc_v4.0.0*filtered_Movement_Regressors.txt )
+num=${#filtered[@]}
+if (( num > 0 )) ; then
+    for filtered_in in ${filtered[@]} ; do
+        TASK=${filtered_in%%/*}  # task name is *top* dirname.
+        if [[ ${TASK} =~ ses- ]] ; then
+            bids_prefix=${subject}_${TASK}
+        elif [[ ${TASK} =~ task- ]] ; then
+            bids_prefix=${subject}_${session}_${TASK}
+        else
+            echo "WARNING: Unable to make a valid bids name from ${TASK}."
+            bids_prefix=${subject}_${TASK}
+        fi
+
+        # Get the filtered motion file for this task.
+        filtered_out=${func}/${bids_prefix}_desc-filtered_motion.tsv
+        tr ' ' '\t' <<< "X Y Z RotX RotY RotZ XDt YDt ZDt RotXDt RotYDt RotZDt" > ${filtered_out}
+        cat ${filtered_in} | tr ' ' '\t' >> ${filtered_out}
+    done
+
+    # If we are here, then there was at least one filtered file. Therefore, the
+    # ptseries **are** filtered, even though the names don't reflect that. So,
+    # while we are in this part of the code, where we know we had at least one
+    # filtered movement regressors file, make the string to be used in the
+    # destination ptseries files (below).
+    ptseries_end="desc-filtered_timeseries.ptseries.nii"
+else
+    # Since there were no filtered movement regressors files, we know that
+    # filtering was not used. The ptseries files are unfiltered.
+    ptseries_end="timeseries.ptseries.nii"
+fi
+
+# There should always be unfiltered motion regressors. Visit each task directory.
+# Get the Atlas time series for each as well.
+for TASK in $( ls -1d *task*/ ) ; do
+    TASK=${TASK%/}
+    if [[ ${TASK} =~ ses- ]] ; then
+        bids_prefix=${subject}_${TASK}
+    elif [[ ${TASK} =~ task- ]] ; then
+        bids_prefix=${subject}_${session}_${TASK}
+    else
+        echo "WARNING: Unable to make a valid bids name from ${TASK}."
+        bids_prefix=${subject}_${TASK}
+    fi
+
+    unfiltered_in="${TASK}/Movement_Regressors.txt"
+    unfiltered_out="${func}/${bids_prefix}_motion.tsv"
+
+    if [ -e ${unfiltered_in} ] ; then
+        # To be valid motion.tsv files, the motion regressors are required to have
+        # column headers and be tab-separated (per BEP012).
+        tr ' ' '\t' <<< "X Y Z RotX RotY RotZ XDt YDt ZDt RotXDt RotYDt RotZDt" > ${unfiltered_out}
+        cat ${unfiltered_in} | tr ' ' '\t' >> ${unfiltered_out}
+    else
+        echo "ERROR: Filemapper is unable to find file ${unfiltered_in}."
+        continue
+    fi
+
+    cp ${TASK}/${TASK}_Atlas.dtseries.nii ${func}/${bids_prefix}_bold_timeseries.dtseries.nii
+done
+
+popd > /dev/null
+shopt -u nullglob
+
+
+fmscript=${FILEMAPPERDIR}/file_mapper_script.py
+CMD="${fmscript} ${TEMPLATE_JSON} -a copy -o -s -sp ${FILES} -dp ${ROOT} -t SUBJECT=${SUB},SESSION=${SES},PIPELINE=${PIPE}"
+set -x
+eval ${CMD}
+set +x
+
+result=$?
+if (( 0 == result )) ; then
+    echo "FileMapper was successful."
+else
+    echo "FileMapper had errors."
+    exit 1
+fi
+
+

Dockerfile

@@ -1,4 +1,4 @@
-FROM dcanlabs/internal-tools:v1.0.1
+FROM dcanlabs/internal-tools:v1.0.2
 
 RUN apt-get update && apt-get install -yq --no-install-recommends \
         apt-utils \
@@ -18,8 +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 'v0.0.9' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan-infant-pipeline.git /opt/pipeline
-RUN git clone -b 'master' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan-infant-pipeline.git /opt/pipeline
+RUN git clone -b 'v0.0.9' --single-branch --depth 1 https://github.com/DCAN-Labs/dcan-infant-pipeline.git /opt/pipeline
 
 
 # unless otherwise specified...
@@ -35,6 +34,11 @@ RUN mkdir /bids_input /output /atlases
 COPY ["./baby_BIDS_cleaning.json", "/opt/dcan-tools/customclean/"]
 COPY ["./baby_BIDS_no_session_cleaning.json", "/opt/dcan-tools/customclean/"]
 
+# Copy file mapper files.
+COPY ["./current_infant.json", "/opt/dcan-tools/filemapper/"]
+COPY ["./current_infant_no_session.json", "/opt/dcan-tools/filemapper/"]
+COPY ["./BIDS_filemapper_wrapper.sh", "/opt/dcan-tools/filemapper/"]
+
 # setup ENTRYPOINT
 COPY ["./entrypoint.sh", "/entrypoint.sh"]
 COPY ["./SetupEnv.sh", "/SetupEnv.sh"]

SetupEnv.sh

@@ -46,6 +46,7 @@ export MATLAB_PREFDIR=/opt/mcr
 export ABCDTASKPREPDIR=/opt/dcan-tools/ABCD_tfMRI
 export CUSTOMCLEANDIR=/opt/dcan-tools/customclean
 export CUSTOMCLEAN_JSON=${CUSTOMCLEANDIR}/baby_BIDS_cleaning.json
+export FILEMAPPERDIR=/opt/dcan-tools/filemapper
 
 
 # hacky solution for now...

app/pipeline_expected_outputs.json

@@ -234,6 +234,8 @@
   ],
   "ExecutiveSummary": [
   ],
+  "FileMapper": [
+  ],
   "CustomClean": [
     "{path}/custom_clean_success_record.txt"
   ]

app/pipelines.py

@@ -1125,12 +1125,12 @@ def args(self):
 
 class FileMapper(Stage):
 
-    script = '{FILEMAPPERDIR}/filemapper_wrapper.sh'
+    script = '{FILEMAPPERDIR}/BIDS_filemapper_wrapper.sh'
 
-    spec = ' --output-root={path}' \
-           ' --participant-label={subject}' \
-           ' --session-id={session}' \
-           ' --json={input_json}'
+    spec = '{subject} ' \
+           '{session} ' \
+           '{path} ' \
+           '{input_json} '
 
     def __init__(self, config, input_json):
         super(__class__, self).__init__(config)

current_infant.json

@@ -0,0 +1,30 @@
+{
+  "DCANBOLDProc_v4.0.0/analyses_v2/motion/ses-{SESSION}_task-rest_run-_power_2014_FD_only.mat": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_ses-{SESSION}_task-rest_motion_mask.mat",
+  "MNINonLinear/Results/ses-{SESSION}_task-rest_run-_DCANBOLDProc_v4.0.0_Atlas.dtseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_ses-{SESSION}_task-rest_bold_timeseries.dtseries.nii",
+  "MNINonLinear/Results/ses-{SESSION}_task-rest_run-_DCANBOLDProc_v4.0.0_Gordon.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_ses-{SESSION}_task-rest_bold_atlas-Gordon2014FreeSurfer_timeseries.ptseries.nii",
+  "MNINonLinear/Results/ses-{SESSION}_task-rest_run-_DCANBOLDProc_v4.0.0_Gordon_subcorticals.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_ses-{SESSION}_task-rest_bold_atlas-Gordon2014FreeSurferSubcortical_timeseries.ptseries.nii",
+  "MNINonLinear/Results/ses-{SESSION}_task-rest_run-_DCANBOLDProc_v4.0.0_HCP.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_ses-{SESSION}_task-rest_bold_atlas-HCP2016FreeSurfer_timeseries.ptseries.nii",
+  "MNINonLinear/Results/ses-{SESSION}_task-rest_run-_DCANBOLDProc_v4.0.0_HCP_subcorticals.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_ses-{SESSION}_task-rest_bold_atlas-HCP2016FreeSurferSubcortical_timeseries.ptseries.nii",
+  "MNINonLinear/Results/ses-{SESSION}_task-rest_run-_DCANBOLDProc_v4.0.0_Markov.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_ses-{SESSION}_task-rest_bold_atlas-Markov2016FreeSurfer_timeseries.ptseries.nii",
+  "MNINonLinear/Results/ses-{SESSION}_task-rest_run-_DCANBOLDProc_v4.0.0_Markov_subcorticals.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_ses-{SESSION}_task-rest_bold_atlas-Markov2016FreeSurferSubcortical_timeseries.ptseries.nii",
+  "MNINonLinear/Results/ses-{SESSION}_task-rest_run-_DCANBOLDProc_v4.0.0_Power.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_ses-{SESSION}_task-rest_bold_atlas-Power2016FreeSurfer_timeseries.ptseries.nii",
+  "MNINonLinear/Results/ses-{SESSION}_task-rest_run-_DCANBOLDProc_v4.0.0_Power_subcorticals.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_ses-{SESSION}_task-rest_bold_atlas-Power2016FreeSurferSubcortical_timeseries.ptseries.nii",
+  "MNINonLinear/Results/ses-{SESSION}_task-rest_run-_DCANBOLDProc_v4.0.0_Yeo.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_ses-{SESSION}_task-rest_bold_atlas-Yeo2016FreeSurfer_timeseries.ptseries.nii",
+  "MNINonLinear/Results/ses-{SESSION}_task-rest_run-_DCANBOLDProc_v4.0.0_Yeo_subcorticals.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_ses-{SESSION}_task-rest_bold_atlas-Yeo2016FreeSurferSubcortical_timeseries.ptseries.nii",
+  "MNINonLinear/fsaverage_LR32k/{SUBJECT}.curvature.32k_fs_LR.dscalar.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_ses-{SESSION}_space-fsLR32k_curv.dscalar.nii",
+  "MNINonLinear/fsaverage_LR32k/{SUBJECT}.sulc.32k_fs_LR.dscalar.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_ses-{SESSION}_space-fsLR32k_sulc.dscalar.nii",
+  "MNINonLinear/fsaverage_LR32k/{SUBJECT}.thickness.32k_fs_LR.dscalar.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_ses-{SESSION}_space-fsLR32k_thickness.dscalar.nii",
+  "MNINonLinear/fsaverage_LR32k/{SUBJECT}.L.midthickness.32k_fs_LR.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_ses-{SESSION}_hemi-L_space-MNI_mesh-fsLR32k_midthickness.surf.gii",
+  "MNINonLinear/fsaverage_LR32k/{SUBJECT}.R.midthickness.32k_fs_LR.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_ses-{SESSION}_hemi-R_space-MNI_mesh-fsLR32k_midthickness.surf.gii",
+  "MNINonLinear/{SUBJECT}.L.midthickness.164k_fs_LR.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_ses-{SESSION}_hemi-L_space-MNI_mesh-fsLR164k_midthickness.surf.gii",
+  "MNINonLinear/{SUBJECT}.R.midthickness.164k_fs_LR.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_ses-{SESSION}_hemi-R_space-MNI_mesh-fsLR164k_midthickness.surf.gii",
+  "MNINonLinear/Native/{SUBJECT}.L.midthickness.native.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_ses-{SESSION}_hemi-L_space-MNI_mesh-native_midthickness.surf.gii",
+  "MNINonLinear/Native/{SUBJECT}.R.midthickness.native.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_ses-{SESSION}_hemi-R_space-MNI_mesh-native_midthickness.surf.gii",
+  "T1w/fsaverage_LR32k/{SUBJECT}.L.midthickness.32k_fs_LR.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_ses-{SESSION}_hemi-L_space-T1w_mesh-fsLR32k_midthickness.surf.gii",
+  "T1w/fsaverage_LR32k/{SUBJECT}.R.midthickness.32k_fs_LR.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_ses-{SESSION}_hemi-R_space-T1w_mesh-fsLR32k_midthickness.surf.gii",
+  "T1w/Native/{SUBJECT}.L.midthickness.native.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_ses-{SESSION}_hemi-L_space-T1w_mesh-native_midthickness.surf.gii",
+  "T1w/Native/{SUBJECT}.R.midthickness.native.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_ses-{SESSION}_hemi-R_space-T1w_mesh-native_midthickness.surf.gii",
+  "T1w/aparc+aseg.nii.gz": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_ses-{SESSION}_space-ACPC_dseg.nii.gz",
+  "MNINonLinear/fsaverage_LR32k/{SUBJECT}.MyelinMap.32k_fs_LR.dscalar.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_ses-{SESSION}_atlas-MNI_space-fsLR32k_myelinmap.dscalar.nii",
+  "MNINonLinear/fsaverage_LR32k/{SUBJECT}.SmoothedMyelinMap.32k_fs_LR.dscalar.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_ses-{SESSION}_atlas-MNI_space-fsLR32k_desc-smoothed_myelinmap.dscalar.nii"
+}

current_infant_no_session.json

@@ -0,0 +1,30 @@
+{
+  "DCANBOLDProc_v4.0.0/analyses_v2/motion/task-rest_run-_power_2014_FD_only.mat": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_task-rest_motion_mask.mat",
+  "MNINonLinear/Results/task-rest_run-_DCANBOLDProc_v4.0.0_Atlas.dtseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_task-rest_bold_timeseries.dtseries.nii",
+  "MNINonLinear/Results/task-rest_run-_DCANBOLDProc_v4.0.0_Gordon.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_task-rest_bold_atlas-Gordon2014FreeSurfer_timeseries.ptseries.nii",
+  "MNINonLinear/Results/task-rest_run-_DCANBOLDProc_v4.0.0_Gordon_subcorticals.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_task-rest_bold_atlas-Gordon2014FreeSurferSubcortical_timeseries.ptseries.nii",
+  "MNINonLinear/Results/task-rest_run-_DCANBOLDProc_v4.0.0_HCP.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_task-rest_bold_atlas-HCP2016FreeSurfer_timeseries.ptseries.nii",
+  "MNINonLinear/Results/task-rest_run-_DCANBOLDProc_v4.0.0_HCP_subcorticals.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_task-rest_bold_atlas-HCP2016FreeSurferSubcortical_timeseries.ptseries.nii",
+  "MNINonLinear/Results/task-rest_run-_DCANBOLDProc_v4.0.0_Markov.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_task-rest_bold_atlas-Markov2016FreeSurfer_timeseries.ptseries.nii",
+  "MNINonLinear/Results/task-rest_run-_DCANBOLDProc_v4.0.0_Markov_subcorticals.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_task-rest_bold_atlas-Markov2016FreeSurferSubcortical_timeseries.ptseries.nii",
+  "MNINonLinear/Results/task-rest_run-_DCANBOLDProc_v4.0.0_Power.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_task-rest_bold_atlas-Power2016FreeSurfer_timeseries.ptseries.nii",
+  "MNINonLinear/Results/task-rest_run-_DCANBOLDProc_v4.0.0_Power_subcorticals.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_task-rest_bold_atlas-Power2016FreeSurferSubcortical_timeseries.ptseries.nii",
+  "MNINonLinear/Results/task-rest_run-_DCANBOLDProc_v4.0.0_Yeo.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_task-rest_bold_atlas-Yeo2016FreeSurfer_timeseries.ptseries.nii",
+  "MNINonLinear/Results/task-rest_run-_DCANBOLDProc_v4.0.0_Yeo_subcorticals.ptseries.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/func/sub-{SUBJECT}_task-rest_bold_atlas-Yeo2016FreeSurferSubcortical_timeseries.ptseries.nii",
+  "MNINonLinear/fsaverage_LR32k/{SUBJECT}.curvature.32k_fs_LR.dscalar.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_space-fsLR32k_curv.dscalar.nii",
+  "MNINonLinear/fsaverage_LR32k/{SUBJECT}.sulc.32k_fs_LR.dscalar.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_space-fsLR32k_sulc.dscalar.nii",
+  "MNINonLinear/fsaverage_LR32k/{SUBJECT}.thickness.32k_fs_LR.dscalar.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_space-fsLR32k_thickness.dscalar.nii",
+  "MNINonLinear/fsaverage_LR32k/{SUBJECT}.L.midthickness.32k_fs_LR.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_hemi-L_space-MNI_mesh-fsLR32k_midthickness.surf.gii",
+  "MNINonLinear/fsaverage_LR32k/{SUBJECT}.R.midthickness.32k_fs_LR.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_hemi-R_space-MNI_mesh-fsLR32k_midthickness.surf.gii",
+  "MNINonLinear/{SUBJECT}.L.midthickness.164k_fs_LR.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_hemi-L_space-MNI_mesh-fsLR164k_midthickness.surf.gii",
+  "MNINonLinear/{SUBJECT}.R.midthickness.164k_fs_LR.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_hemi-R_space-MNI_mesh-fsLR164k_midthickness.surf.gii",
+  "MNINonLinear/Native/{SUBJECT}.L.midthickness.native.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_hemi-L_space-MNI_mesh-native_midthickness.surf.gii",
+  "MNINonLinear/Native/{SUBJECT}.R.midthickness.native.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_hemi-R_space-MNI_mesh-native_midthickness.surf.gii",
+  "T1w/fsaverage_LR32k/{SUBJECT}.L.midthickness.32k_fs_LR.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_hemi-L_space-T1w_mesh-fsLR32k_midthickness.surf.gii",
+  "T1w/fsaverage_LR32k/{SUBJECT}.R.midthickness.32k_fs_LR.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_hemi-R_space-T1w_mesh-fsLR32k_midthickness.surf.gii",
+  "T1w/Native/{SUBJECT}.L.midthickness.native.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_hemi-L_space-T1w_mesh-native_midthickness.surf.gii",
+  "T1w/Native/{SUBJECT}.R.midthickness.native.surf.gii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_hemi-R_space-T1w_mesh-native_midthickness.surf.gii",
+  "T1w/aparc+aseg.nii.gz": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_space-ACPC_dseg.nii.gz",
+  "MNINonLinear/fsaverage_LR32k/{SUBJECT}.MyelinMap.32k_fs_LR.dscalar.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_atlas-MNI_space-fsLR32k_myelinmap.dscalar.nii",
+  "MNINonLinear/fsaverage_LR32k/{SUBJECT}.SmoothedMyelinMap.32k_fs_LR.dscalar.nii": "derivatives/{PIPELINE}/sub-{SUBJECT}/ses-{SESSION}/anat/sub-{SUBJECT}_atlas-MNI_space-fsLR32k_desc-smoothed_myelinmap.dscalar.nii"
+}