NF: Output BOLD HMC transforms and reference volume [skip ds005][skip…

… ds210]

.circleci/ds005_bids_fasttrack_outputs.txt

@@ -10,16 +10,20 @@ bids/logs/CITATION.md
 bids/logs/CITATION.tex
 bids/sub-01
 bids/sub-01/func
+bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_boldref.nii.gz
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
+bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-boldref_mode-image_xfm.txt
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-T1w_mode-image_xfm.txt
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-T1w_to-scanner_mode-image_xfm.txt
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.func.gii
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.json
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.func.gii
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
+bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_boldref.nii.gz
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
+bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-boldref_mode-image_xfm.txt
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii

.circleci/ds005_bids_outputs.txt

@@ -33,16 +33,20 @@ bids/sub-01/anat/sub-01_label-CSF_probseg.nii.gz
 bids/sub-01/anat/sub-01_label-GM_probseg.nii.gz
 bids/sub-01/anat/sub-01_label-WM_probseg.nii.gz
 bids/sub-01/func
+bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_boldref.nii.gz
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
+bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-boldref_mode-image_xfm.txt
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-T1w_mode-image_xfm.txt
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-T1w_to-scanner_mode-image_xfm.txt
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.func.gii
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.json
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.func.gii
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
+bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_boldref.nii.gz
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
+bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-boldref_mode-image_xfm.txt
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii

.circleci/ds005_legacy_fasttrack_outputs.txt

@@ -10,8 +10,10 @@ fmriprep/logs/CITATION.md
 fmriprep/logs/CITATION.tex
 fmriprep/sub-01
 fmriprep/sub-01/func
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_boldref.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-boldref_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.func.gii
@@ -22,8 +24,10 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_boldref.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-boldref_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii

.circleci/ds005_legacy_outputs.txt

@@ -33,8 +33,10 @@ fmriprep/sub-01/anat/sub-01_label-CSF_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_label-GM_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_label-WM_probseg.nii.gz
 fmriprep/sub-01/func
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_boldref.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-boldref_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.func.gii
@@ -45,8 +47,10 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_boldref.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-boldref_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii

.circleci/ds005_legacy_partial_fasttrack_outputs.txt

@@ -17,9 +17,11 @@ fmriprep/sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
 fmriprep/sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_boldref.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-MELODIC_mixing.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-boldref_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii

.circleci/ds005_legacy_partial_outputs.txt

@@ -58,9 +58,11 @@ fmriprep/sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
 fmriprep/sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_boldref.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-MELODIC_mixing.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-boldref_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii

.circleci/ds054_fasttrack_outputs.txt

@@ -25,6 +25,7 @@ fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-confounds_times
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-confounds_timeseries.tsv
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_from-scanner_to-boldref_mode-image_xfm.txt
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
@@ -48,6 +49,7 @@ fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-confounds_times
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-confounds_timeseries.tsv
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_from-scanner_to-boldref_mode-image_xfm.txt
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz

.circleci/ds054_outputs.txt

@@ -44,6 +44,7 @@ fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-confounds_times
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-confounds_timeseries.tsv
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_from-scanner_to-boldref_mode-image_xfm.txt
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
@@ -67,6 +68,7 @@ fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-confounds_times
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-confounds_timeseries.tsv
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.nii.gz
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_from-scanner_to-boldref_mode-image_xfm.txt
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz

.circleci/ds210_fasttrack_outputs.txt

@@ -25,6 +25,7 @@ fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.json
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.nii.gz
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.json
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.nii.gz
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-scanner_to-boldref_mode-image_xfm.txt
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.json

.circleci/ds210_outputs.txt

@@ -44,6 +44,7 @@ fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.json
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.nii.gz
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.json
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.nii.gz
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-scanner_to-boldref_mode-image_xfm.txt
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.json

fmriprep/workflows/bold/base.py

@@ -121,6 +121,8 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
         Affine transform from BOLD reference space to T1w space
     anat2bold_xfm
         Affine transform from T1w space to BOLD reference space
+    hmc_xforms
+        Affine transforms for each BOLD volume to the BOLD reference
     bold_mask_t1
         BOLD series mask in T1w space
     bold_aseg_t1
@@ -369,6 +371,7 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
                 "bold_t1_ref",
                 "bold2anat_xfm",
                 "anat2bold_xfm",
+                "hmc_xforms",
                 "bold_mask_t1",
                 "bold_aseg_t1",
                 "bold_aparc_t1",
@@ -453,6 +456,7 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
             ("bold_t1_ref", "inputnode.bold_t1_ref"),
             ("bold2anat_xfm", "inputnode.bold2anat_xfm"),
             ("anat2bold_xfm", "inputnode.anat2bold_xfm"),
+            ("hmc_xforms", "inputnode.hmc_xforms"),
             ("bold_aseg_t1", "inputnode.bold_aseg_t1"),
             ("bold_aparc_t1", "inputnode.bold_aparc_t1"),
             ("bold_mask_t1", "inputnode.bold_mask_t1"),
@@ -622,6 +626,9 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
             ("outputnode.raw_ref_image", "inputnode.raw_ref_image"),
             ("outputnode.bold_file", "inputnode.bold_file"),
         ]),
+        (bold_hmc_wf, outputnode, [
+            ("outputnode.xforms", "hmc_xforms"),
+        ]),
         # EPI-T1w registration workflow
         (inputnode, bold_reg_wf, [
             ("t1w_dseg", "inputnode.t1w_dseg"),

fmriprep/workflows/bold/outputs.py

@@ -220,6 +220,7 @@ def init_func_derivatives_wf(
                 't2star_std',
                 'bold2anat_xfm',
                 'anat2bold_xfm',
+                'hmc_xforms',
                 'acompcor_masks',
                 'tcompcor_mask',
             ]
@@ -280,6 +281,40 @@ def init_func_derivatives_wf(
     ])
     # fmt:on
 
+    # Output HMC and reference volume
+    ds_bold_hmc_xfm = pe.Node(
+        DerivativesDataSink(
+            base_directory=output_dir,
+            to='boldref',
+            mode='image',
+            suffix='xfm',
+            extension='.txt',
+            dismiss_entities=('echo',),
+            **{'from': 'scanner'},
+        ),
+        name='ds_bold_hmc_xfm',
+        run_without_submitting=True,
+        mem_gb=DEFAULT_MEMORY_MIN_GB,
+    )
+
+    ds_bold_native_ref = pe.Node(
+        DerivativesDataSink(
+            base_directory=output_dir, suffix='boldref', compress=True, dismiss_entities=("echo",)
+        ),
+        name='ds_bold_native_ref',
+        run_without_submitting=True,
+        mem_gb=DEFAULT_MEMORY_MIN_GB,
+    )
+
+    # fmt:off
+    workflow.connect([
+        (inputnode, ds_bold_hmc_xfm, [('source_file', 'source_file'),
+                                      ('hmc_xforms', 'in_file')]),
+        (inputnode, ds_bold_native_ref, [('source_file', 'source_file'),
+                                         ('bold_native_ref', 'in_file')])
+    ])
+    # fmt:on
+
     bold_output = nonstd_spaces.intersection(('func', 'run', 'bold', 'boldref', 'sbref'))
     if bold_output:
         ds_bold_native = pe.Node(
@@ -304,17 +339,6 @@ def init_func_derivatives_wf(
 
     # Save masks and boldref if we're going to save either orig BOLD series or echos
     if bold_output or multiecho and config.execution.me_output_echos:
-        ds_bold_native_ref = pe.Node(
-            DerivativesDataSink(
-                base_directory=output_dir,
-                suffix='boldref',
-                compress=True,
-                dismiss_entities=("echo",),
-            ),
-            name='ds_bold_native_ref',
-            run_without_submitting=True,
-            mem_gb=DEFAULT_MEMORY_MIN_GB,
-        )
         ds_bold_mask_native = pe.Node(
             DerivativesDataSink(
                 base_directory=output_dir,
@@ -329,8 +353,6 @@ def init_func_derivatives_wf(
         )
         # fmt:off
         workflow.connect([
-            (inputnode, ds_bold_native_ref, [('source_file', 'source_file'),
-                                             ('bold_native_ref', 'in_file')]),
             (inputnode, ds_bold_mask_native, [('source_file', 'source_file'),
                                               ('bold_mask_native', 'in_file')]),
             (raw_sources, ds_bold_mask_native, [('out', 'RawSources')]),