diff --git a/fmriprep/workflows/bold/outputs.py b/fmriprep/workflows/bold/outputs.py index df8de999c..f8c9ebbb3 100644 --- a/fmriprep/workflows/bold/outputs.py +++ b/fmriprep/workflows/bold/outputs.py @@ -163,25 +163,33 @@ def init_func_fit_reports_wf( Inputs ------ - std_t1w - T1w image resampled to standard space - std_mask - Mask of skull-stripped template - subject_dir - FreeSurfer SUBJECTS_DIR - subject_id - FreeSurfer subject ID - t1w_conform_report - Conformation report + sdc_boldref + BOLD reference before SDC, in BOLD space + coreg_boldref + BOLD reference after SDC, in BOLD space + boldref2anat_xfm + Affine transform from BOLD reference to anatomical space + boldref2fmap_xfm + Affine transform from BOLD reference to fieldmap space t1w_preproc The T1w reference map, which is calculated as the average of bias-corrected and preprocessed T1w images, defining the anatomical space. - t1w_dseg - Segmentation in T1w space t1w_mask Brain (binary) mask estimated by brain extraction. - template - Template space and specifications + t1w_dseg + Segmentation in T1w space + fieldmap + Reconstructed fieldmap, in BOLD space + fmap_ref + Fieldmap reference image, in fieldmap space + subject_dir + FreeSurfer SUBJECTS_DIR + subject_id + FreeSurfer subject ID + summary_report + HTML snippet summarizing BOLD processing decisions + validation_report + HTML snippet indicating whether affine metadata were overwritten """ from nireports.interfaces.reporting.base import ( @@ -313,18 +321,6 @@ def init_func_fit_reports_wf( mem_gb=1, ) - fmap_boldref = pe.Node( - ApplyTransforms( - dimension=3, - default_value=0, - float=True, - invert_transform_flags=[True], - interpolation='LanczosWindowedSinc', - ), - name='fmap_boldref', - mem_gb=1, - ) - # SDC1 sdcreg_report = pe.Node( FieldmapReportlet( @@ -377,17 +373,12 @@ def init_func_fit_reports_wf( ('coreg_boldref', 'reference_image'), ('boldref2fmap_xfm', 'transforms'), ]), - (inputnode, fmap_boldref, [ - ('fieldmap', 'input_image'), - ('coreg_boldref', 'reference_image'), - ('boldref2fmap_xfm', 'transforms'), - ]), (inputnode, sdcreg_report, [ ('sdc_boldref', 'reference'), + ('fieldmap', 'fieldmap'), ('bold_mask', 'mask'), ]), (fmapref_boldref, sdcreg_report, [('output_image', 'moving')]), - (fmap_boldref, sdcreg_report, [('output_image', 'fieldmap')]), (sdcreg_report, ds_sdcreg_report, [('out_report', 'in_file')]), (inputnode, sdc_report, [ ('sdc_boldref', 'before'),