From 18d6b65375f6e3a6fe2928791f36444cf5ed206c Mon Sep 17 00:00:00 2001 From: Florian Rupprecht Date: Fri, 6 Feb 2026 15:42:11 -0500 Subject: [PATCH 1/5] Add initial pipeline flow graphic draft --- docs/pipeline_flow.svg | 2025 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 2025 insertions(+) create mode 100644 docs/pipeline_flow.svg diff --git a/docs/pipeline_flow.svg b/docs/pipeline_flow.svg new file mode 100644 index 00000000..41b7bdb3 --- /dev/null +++ b/docs/pipeline_flow.svg @@ -0,0 +1,2025 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + RBC Processing Pipeline + + Anatomical & functional preprocessing · Single-step resampling · Nuisance regression · Metrics + + + + + T1w Anatomical + + + + + + + BOLD Functional + + + Anatomical + + + + Brain Extraction + ANTs · N4 bias field correction + Registration to OASIS template · mask at p > 0.5 + + + + + Tissue Segmentation + FSL FAST · 3-class (CSF / GM / WM) + Probability maps thresholded at 0.95 + + + + + Register to MNI-152 + ANTs · Rigid → Affine → SyN + LanczosWindowedSinc interpolation + + + + + + + Functional + + + + + + Motion Correction + FSL mcflirt · 6 DOF rigid-body + Reference: middle volume + + + + + + + + + + + Despike + Slice Timing + AFNI 3dDespike · 3dTshift + Timing from BIDS SliceTiming metadata + + + + + + + + Brain Masking + FSL BET + AFNI hybrid + Dilated intersection mask + + + + + + + + WM boundary + tissue masks + motion params + + Coregistration · Resampling + + + + + + + + + BOLD → T1w Coregistration + FSL FLIRT · 6 DOF · boundary-based registration with WM segment + + + + + + + + + + + Single-Step Resample → MNI 2 mm + All transforms composed (motion + distortion + coreg + warp) · one interpolation + + + Nuisance Regression + + + + + + + Confound Removal + Bandpass Filtering + 36-parameter or aCompCor regression · AFNI 3dTproject + Bandpass 0.01 – 0.1 Hz · template-space despiking (2nd pass) + + + Metrics + + + + ALFF / fALFF + Low-frequency fluctuationamplitude + + + + + ReHo + Kendall's W ·27-voxel neighborhood + + + + + + + + + + + + + + + Centrality + Degree centrality · lFCD + + + + + Timeseries + FC + Schaefer · AAL · HO · Glasser … + + + + + + + + + + + + + + + + + + Spatial Smoothing + Z-Scoring + AFNI 3dBlurToFWHM · 6 mm FWHM · voxelwise standardization + + + + + Quality Control + + + + + Motion Metrics + FD · DVARS · RMS + + + + + + + Registration + Dice · Jaccard · CC + + + Pass / Fail + + + + + + + + + Outputs + Cleaned BOLD · Derivative maps (ALFF · ReHo · Centrality) · Timeseries · Correlation matrices · QC TSV + + + TOOLS + + ANTs + + FSL + + AFNI + + Python (nibabel · numpy) + + + cross-stream dependency + + From 5a404c6393683e0c6df466c1d887258f6ab31634 Mon Sep 17 00:00:00 2001 From: Florian Rupprecht Date: Fri, 6 Feb 2026 17:10:00 -0500 Subject: [PATCH 2/5] Updates --- docs/pipeline_flow.svg | 1034 ++++++++++++++++++++++++++-------------- 1 file changed, 671 insertions(+), 363 deletions(-) diff --git a/docs/pipeline_flow.svg b/docs/pipeline_flow.svg index 41b7bdb3..2db257ec 100644 --- a/docs/pipeline_flow.svg +++ b/docs/pipeline_flow.svg @@ -20,9 +20,9 @@ inkscape:pageopacity="0.0" inkscape:pagecheckerboard="0" inkscape:deskcolor="#d1d1d1" - inkscape:zoom="0.68389831" - inkscape:cx="371.40025" - inkscape:cy="394.06444" + inkscape:zoom="0.96717827" + inkscape:cx="500.42481" + inkscape:cy="111.14807" inkscape:window-width="1920" inkscape:window-height="1009" inkscape:window-x="1912" @@ -110,10 +110,10 @@ + x="-inf" + y="-inf" + width="inf" + height="inf"> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - RBC Processing Pipeline - - Anatomical & functional preprocessing · Single-step resampling · Nuisance regression · Metrics + + RBC Processing Pipeline + Anatomical & functional preprocessing · Single-step resampling · Nuisance regression · Metrics + + transform="translate(-10.458476,8)"> + transform="translate(-13.382887,7.2688971)"> + transform="translate(-1.3196904,8)"> + transform="translate(-1.3196904,8)"> Probability maps thresholded at 0.95 - - - - Register to MNI-152 - ANTs · Rigid → Affine → SyN - LanczosWindowedSinc interpolation - + + + Register to MNI-152-NLin6Asym + ANTs · Rigid → Affine → SyN + LanczosWindowedSinc interpolation + transform="translate(-1.3196904,8)"> Reference: middle volume + - + id="g18" + transform="translate(1.2651485,2.5848389)"> + transform="translate(580,259)" + id="g74" + style="filter:url(#card)"> + id="text75" + style="filter:url(#card)" + transform="rotate(90,590.12881,278.6159)">→ + transform="translate(580,283.60099)" + id="g75" + style="filter:url(#card)"> - Despike + Slice Timing - AFNI 3dDespike · 3dTshift - Timing from BIDS SliceTiming metadata + Despike + Slice Timing + AFNI 3dDespike · 3dTshift + Timing from BIDS SliceTiming metadata + transform="translate(-1.3196904,8)"> WM boundary + id="tspan2">WM boundary tissue masks motion params Coregistration · Resampling + transform="translate(-1.3196904,8)"> FSL FLIRT · 6 DOF · boundary-based registration with WM segment - - - - - - - - - - Single-Step Resample → MNI 2 mm - All transforms composed (motion + distortion + coreg + warp) · one interpolation - + + Single-Step Resample → 2 mm + All transforms composed (motion + distortion + coreg + warp) · one interpolation + + + + Nuisance Regression Confound Removal + Bandpass Filtering 36-parameter or aCompCor regression · AFNI 3dTproject Bandpass 0.01 – 0.1 Hz · template-space despiking (2nd pass) + transform="translate(-1.3196904,8)"> + transform="translate(-1.3196904,8)"> + transform="translate(-1.3196904,8)"> + transform="translate(-1.3196904,8)"> + transform="translate(-1.3196904,8)"> Quality Control Motion Metrics FD · DVARS · RMS Registration - + transform="translate(-1.3196904,8)"> Cleaned BOLD · Derivative maps (ALFF · ReHo · Centrality) · Timeseries · Correlation matrices · QC TSV + - TOOLS - - ANTs - - FSL - - AFNI - - Python (nibabel · numpy) - + id="g19"> cross-stream dependency + style="letter-spacing:0.08em;opacity:0.55" + id="text135">TOOLS + + ANTs + + FSL + + AFNI + + Python (nibabel · numpy) + + + cross-stream dependency + + + + + + + + + + From 5f7ad6fcb42b638cbd5de357b698e4182ba458e9 Mon Sep 17 00:00:00 2001 From: Florian Rupprecht Date: Fri, 6 Feb 2026 17:13:00 -0500 Subject: [PATCH 3/5] Minor change to mni label --- docs/pipeline_flow.svg | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/pipeline_flow.svg b/docs/pipeline_flow.svg index 2db257ec..91933f89 100644 --- a/docs/pipeline_flow.svg +++ b/docs/pipeline_flow.svg @@ -20,9 +20,9 @@ inkscape:pageopacity="0.0" inkscape:pagecheckerboard="0" inkscape:deskcolor="#d1d1d1" - inkscape:zoom="0.96717827" - inkscape:cx="500.42481" - inkscape:cy="111.14807" + inkscape:zoom="0.68389831" + inkscape:cx="500.07435" + inkscape:cy="598.77323" inkscape:window-width="1920" inkscape:window-height="1009" inkscape:window-x="1912" @@ -1194,7 +1194,7 @@ font-weight="600" fill="#1e293b" id="text67" - style="filter:url(#card)">Register to MNI-152-NLin6Asym + style="filter:url(#card)">Register to MNI152NLin6Asym Date: Mon, 9 Feb 2026 13:59:58 -0500 Subject: [PATCH 4/5] Whatever --- docs/pipeline_flow.svg | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/pipeline_flow.svg b/docs/pipeline_flow.svg index 91933f89..2458c765 100644 --- a/docs/pipeline_flow.svg +++ b/docs/pipeline_flow.svg @@ -7,6 +7,9 @@ id="svg141" sodipodi:docname="pipeline_flow.svg" inkscape:version="1.4.2 (f4327f4, 2025-05-13)" + inkscape:export-filename="pipeline_flow.png" + inkscape:export-xdpi="162.71187" + inkscape:export-ydpi="162.71187" xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd" xmlns="http://www.w3.org/2000/svg" @@ -28,7 +31,8 @@ inkscape:window-x="1912" inkscape:window-y="-8" inkscape:window-maximized="1" - inkscape:current-layer="svg141" /> + inkscape:current-layer="svg141" + inkscape:export-bgcolor="#ffffffff" /> Date: Wed, 11 Feb 2026 18:33:24 -0500 Subject: [PATCH 5/5] Remove centrality; Add gradients; tighter layout --- docs/pipeline_flow.svg | 1659 +++++++++++++--------------------------- 1 file changed, 546 insertions(+), 1113 deletions(-) diff --git a/docs/pipeline_flow.svg b/docs/pipeline_flow.svg index 2458c765..97bd1cdd 100644 --- a/docs/pipeline_flow.svg +++ b/docs/pipeline_flow.svg @@ -1,8 +1,8 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - RBC Processing Pipeline - RBC Processing PipelineAnatomical & functional preprocessing · Single-step resampling · Nuisance regression · Metrics - - - Anatomical & functional preprocessing · Single-step resampling · Nuisance regression · Metrics - - - T1w Anatomical - - T1w Anatomical - - - - - BOLD Functional - - - BOLD FunctionalAnatomical - Anatomical - - - Brain Extraction - Brain ExtractionANTs · N4 bias field correction - ANTs · N4 bias field correctionRegistration to OASIS template · mask at p > 0.5 - - Registration to OASIS template · mask at p > 0.5 - - - Tissue Segmentation - Tissue SegmentationFSL FAST · 3-class (CSF / GM / WM) - FSL FAST · 3-class (CSF / GM / WM)Probability maps thresholded at 0.95 - - Probability maps thresholded at 0.95 - - Register to MNI152NLin6Asym - Register to MNI152NLin6AsymANTs · Rigid → Affine → SyN - ANTs · Rigid → Affine → SyNLanczosWindowedSinc interpolation - - - - - - LanczosWindowedSinc interpolationFunctional - Functional - - - - - Motion Correction - Motion CorrectionFSL mcflirt · 6 DOF rigid-body - FSL mcflirt · 6 DOF rigid-bodyReference: middle volume - - Reference: middle volume - - - - - - - - - - Despike + Slice Timing - Despike + Slice TimingAFNI 3dDespike · 3dTshift - AFNI 3dDespike · 3dTshiftTiming from BIDS SliceTiming metadata - Timing from BIDS SliceTiming metadata - - - - - - Brain Masking - Brain MaskingFSL BET + AFNI hybrid - FSL BET + AFNI hybridDilated intersection mask - - - - - - - Dilated intersection mask - WM boundary - WM boundarytissue masks - tissue masksmotion params - - motion paramsCoregistration · Resampling - Coregistration · Resampling - - - - - - - - BOLD → T1w Coregistration - BOLD → T1w CoregistrationFSL FLIRT · 6 DOF · boundary-based registration with WM segment - - FSL FLIRT · 6 DOF · boundary-based registration with WM segment - Single-Step Resample → 2 mm - Single-Step Resample → 2 mmAll transforms composed (motion + distortion + coreg + warp) · one interpolation - All transforms composed (motion + distortion + coreg + warp) · one interpolation - - - - - Nuisance Regression - Nuisance Regression - - - - - - Confound Removal + Bandpass Filtering - Confound Removal + Bandpass Filtering36-parameter or aCompCor regression · AFNI 3dTproject - 36-parameter or aCompCor regression · AFNI 3dTprojectBandpass 0.01 – 0.1 Hz · template-space despiking (2nd pass) - Bandpass 0.01 – 0.1 Hz · template-space despiking (2nd pass) - - Metrics - Metrics - - - ALFF / fALFF - ALFF / fALFFamplitude - - amplitude - - - ReHo - ReHo27-voxel neighborhood - - 27-voxel neighborhood - - - - - - - - - - - - - Centrality - GradientDegree centrality · lFCD - - PCA · Brainspace - - - Timeseries + FC - Timeseries + FCSchaefer · AAL · HO · Glasser … - - - Schaefer · AAL · HO · Glasser … - - - - - - - - - - - - - - - Spatial Smoothing + Z-Scoring - Spatial Smoothing + Z-ScoringAFNI 3dBlurToFWHM · 6 mm FWHM · voxelwise standardization - - AFNI 3dBlurToFWHM · 6 mm FWHM · voxelwise standardization - - - Quality Control - Quality Control - - - - Motion Metrics - Motion MetricsFD · DVARS · RMS - FD · DVARS · RMS - - - - - - Registration - RegistrationDice · Jaccard · CC - Dice · Jaccard · CC - - Pass / Fail - Pass / Fail - - - - - - - Outputs - OutputsCleaned BOLD · Derivative maps (ALFF · ReHo · Centrality) · Timeseries · Correlation matrices · QC TSV - - Cleaned BOLD · Derivative maps (ALFF · ReHo · Centrality) · Timeseries · Correlation matrices · QC TSV - - - TOOLS - - ANTs - - FSL - - AFNI - - Python (nibabel · numpy) - - - cross-stream dependency - - - - - - - - - - - - + id="path16-9-6" />