Update things.

PennLINC · Oct 15, 2023 · c560f30 · c560f30
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commit c560f30
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Showing 4 changed files with 25 additions and 37 deletions.
diff --git a/docs/outputs.rst b/docs/outputs.rst
@@ -165,21 +165,15 @@ Denoised or residual BOLD data
    xcp_d/
       sub-<label>/[ses-<label>/]
          func/
-            # Nifti
+            # NIfTI
             <source_entities>_space-<label>_desc-denoised_bold.nii.gz
-            <source_entities>_space-<label>_desc-denoised_bold.json
             <source_entities>_space-<label>_desc-denoisedSmoothed_bold.nii.gz
-            <source_entities>_space-<label>_desc-denoisedSmoothed_bold.json
             <source_entities>_space-<label>_desc-interpolated_bold.nii.gz
-            <source_entities>_space-<label>_desc-interpolated_bold.json
 
-            # Cifti
+            # CIFTI
             <source_entities>_space-fsLR_den-91k_desc-denoised_bold.dtseries.nii
-            <source_entities>_space-fsLR_den-91k_desc-denoised_bold.json
             <source_entities>_space-fsLR_den-91k_desc-denoisedSmoothed_bold.dtseries.nii
-            <source_entities>_space-fsLR_den-91k_desc-denoisedSmoothed_bold.json
             <source_entities>_space-fsLR_den-91k_desc-interpolated_bold.dtseries.nii
-            <source_entities>_space-fsLR_den-91k_desc-interpolated_bold.json
 
 .. important::
 
@@ -212,21 +206,21 @@ This includes the atlases used to extract the timeseries.
 .. code-block::
 
    xcp_d/
-      # Nifti
+      # NIfTI
       space-<label>_atlas-<label>_dseg.nii.gz
 
-      # Cifti
+      # CIFTI
       space-<label>_atlas-<label>_dseg.dlabel.nii
 
       sub-<label>/[ses-<label>/]
          func/
-            # Nifti
+            # NIfTI
             <source_entities>_space-<label>_atlas-<label>_coverage.tsv
             <source_entities>_space-<label>_atlas-<label>_timeseries.tsv
             <source_entities>_space-<label>_atlas-<label>_measure-pearsoncorrelation_conmat.tsv
             <source_entities>_space-<label>_atlas-<label>_measure-pearsoncorrelation_desc-<INT>volumes_conmat.tsv
 
-            # Cifti
+            # CIFTI
             <source_entities>_space-fsLR_atlas-<label>_den-91k_coverage.tsv
             <source_entities>_space-fsLR_atlas-<label>_den-91k_coverage.pscalar.nii
             <source_entities>_space-fsLR_atlas-<label>_den-91k_timeseries.tsv
@@ -259,14 +253,14 @@ data.
    xcp_d/
       sub-<label>/[ses-<label>/]
          func/
-            # Nifti
+            # NIfTI
             <source_entities>_space-<label>_reho.nii.gz
             <source_entities>_space-<label>_alff.nii.gz
             <source_entities>_space-<label>_desc-smooth_alff.nii.gz
             <source_entities>_space-<label>_atlas-<atlas>_alff.tsv
             <source_entities>_space-<label>_atlas-<atlas>_reho.tsv
 
-            # Cifti
+            # CIFTI
             <source_entities>_space-fsLR_den-91k_reho.dscalar.nii
             <source_entities>_space-fsLR_den-91k_alff.dscalar.nii
             <source_entities>_space-fsLR_den-91k_desc-smooth_alff.dscalar.nii
@@ -284,21 +278,15 @@ Other outputs include quality control, framewise displacement, and confounds fil
 
       sub-<label>/[ses-<label>/]
          func/
-            # Nifti
-            <source_entities>_space-<label>_desc-linc_qc.csv
             <source_entities>[_desc-filtered]_motion.tsv
-            <source_entities>[_desc-filtered]_motion.json
             <source_entities>_outliers.tsv
-            <source_entities>_outliers.json
             <source_entities>_design.tsv
 
-            # Cifti
+            # NIfTI
+            <source_entities>_space-<label>_desc-linc_qc.csv
+
+            # CIFTI
             <source_entities>_space-fsLR_desc-linc_qc.csv
-            <source_entities>[_desc-filtered]_motion.tsv
-            <source_entities>[_desc-filtered]_motion.json
-            <source_entities>_outliers.tsv
-            <source_entities>_outliers.json
-            <source_entities>_design.tsv
 
 ``[desc-filtered]_motion.tsv`` is a tab-delimited file with seven columns:
 one for each of the six filtered motion parameters, as well as "framewise_displacement".
@@ -327,10 +315,6 @@ to 1mm FD in 0.01 steps.
    xcp_d/
       sub-<label>/[ses-<label>/]
          func/
-            # Nifti
-            <source_entities>_desc-dcan_qc.hdf5
-
-            # Cifti
             <source_entities>_desc-dcan_qc.hdf5
 
 These files have the following keys:

diff --git a/xcp_d/workflows/base.py b/xcp_d/workflows/base.py
@@ -799,6 +799,7 @@ def init_subject_wf(
                 smoothing=smoothing,
                 cifti=cifti,
                 dcan_qc=dcan_qc,
+                fd_thresh=fd_thresh,
                 mem_gb=1,
                 omp_nthreads=omp_nthreads,
                 name=f"concatenate_entity_set_{ent_set}_wf",

diff --git a/xcp_d/workflows/concatenation.py b/xcp_d/workflows/concatenation.py
@@ -20,14 +20,15 @@
 def init_concatenate_data_wf(
     output_dir,
     motion_filter_type,
-    mem_gb,
-    omp_nthreads,
     TR,
     head_radius,
     params,
     smoothing,
     cifti,
     dcan_qc,
+    fd_thresh,
+    mem_gb,
+    omp_nthreads,
     name="concatenate_data_wf",
 ):
     """Concatenate postprocessed data across runs and directions.
@@ -42,29 +43,31 @@ def init_concatenate_data_wf(
             wf = init_concatenate_data_wf(
                 output_dir=".",
                 motion_filter_type=None,
-                mem_gb=0.1,
-                omp_nthreads=1,
                 TR=2,
                 head_radius=50,
                 params="none",
                 smoothing=None,
                 cifti=False,
                 dcan_qc=True,
+                fd_thresh=0.3,
+                mem_gb=0.1,
+                omp_nthreads=1,
                 name="concatenate_data_wf",
             )
 
     Parameters
     ----------
     %(output_dir)s
     %(motion_filter_type)s
-    %(mem_gb)s
-    %(omp_nthreads)s
     %(TR)s
     %(head_radius)s
     %(params)s
     %(smoothing)s
     %(cifti)s
     %(dcan_qc)s
+    fd_thresh
+    %(mem_gb)s
+    %(omp_nthreads)s
     %(name)s
         Default is "concatenate_data_wf".
 
@@ -440,7 +443,7 @@ def init_concatenate_data_wf(
                 mem_gb=2,
             )
 
-        if dcan_qc:
+        if dcan_qc and (fd_thresh > 0):
             ds_interpolated_filtered_bold = pe.Node(
                 DerivativesDataSink(
                     base_directory=output_dir,
@@ -480,7 +483,7 @@ def init_concatenate_data_wf(
                 mem_gb=2,
             )
 
-        if dcan_qc:
+        if dcan_qc and (fd_thresh > 0):
             ds_interpolated_filtered_bold = pe.Node(
                 DerivativesDataSink(
                     base_directory=output_dir,

diff --git a/xcp_d/workflows/outputs.py b/xcp_d/workflows/outputs.py
@@ -501,7 +501,7 @@ def _custom_to_source(out_file):
     ])
     # fmt:on
 
-    if dcan_qc:
+    if dcan_qc and (fd_thresh > 0):
         ds_interpolated_denoised_bold = pe.Node(
             DerivativesDataSink(
                 base_directory=output_dir,