diff --git a/docs/assets/BrainHack2024/index.html b/docs/talks/BrainHack2024/index.html similarity index 100% rename from docs/assets/BrainHack2024/index.html rename to docs/talks/BrainHack2024/index.html diff --git a/docs/assets/EPFL2023/index.html b/docs/talks/EPFL2023/index.html similarity index 100% rename from docs/assets/EPFL2023/index.html rename to docs/talks/EPFL2023/index.html diff --git a/docs/assets/INCF22-MRIQC/index.html b/docs/talks/INCF22-MRIQC/index.html similarity index 100% rename from docs/assets/INCF22-MRIQC/index.html rename to docs/talks/INCF22-MRIQC/index.html diff --git a/docs/assets/OHBM2022/index.html b/docs/talks/OHBM2022/index.html similarity index 100% rename from docs/assets/OHBM2022/index.html rename to docs/talks/OHBM2022/index.html diff --git a/docs/assets/OHBM2023/QCTalkOHBM23CelineProvins.pdf b/docs/talks/OHBM2023/QCTalkOHBM23CelineProvins.pdf similarity index 100% rename from docs/assets/OHBM2023/QCTalkOHBM23CelineProvins.pdf rename to docs/talks/OHBM2023/QCTalkOHBM23CelineProvins.pdf diff --git a/docs/assets/ORN-Workshop/index.html b/docs/talks/ORN-Workshop/index.html similarity index 100% rename from docs/assets/ORN-Workshop/index.html rename to docs/talks/ORN-Workshop/index.html diff --git a/docs/assets/ORN-Workshop/presentation.md b/docs/talks/ORN-Workshop/presentation.md similarity index 100% rename from docs/assets/ORN-Workshop/presentation.md rename to docs/talks/ORN-Workshop/presentation.md diff --git a/docs/talks/bhd2020/images/card-bids.svg b/docs/talks/bhd2020/images/card-bids.svg new file mode 100644 index 0000000..443e546 --- /dev/null +++ b/docs/talks/bhd2020/images/card-bids.svg @@ -0,0 +1,297 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + BIDS + PyBIDS + Brain Imaging DataStructure + The data specification prescribing the formalstructure for the neuroimaging data inputsand outputs. + + + diff --git a/docs/talks/bhd2020/images/card-crowdmri.svg b/docs/talks/bhd2020/images/card-crowdmri.svg new file mode 100644 index 0000000..4709e6b --- /dev/null +++ b/docs/talks/bhd2020/images/card-crowdmri.svg @@ -0,0 +1,349 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + CrowdMRI + A database of crowdsourcedneuroimaging features + An Internet Service endpoint to collect statisticsabout data quality, extensible to any crowdsourcingapplication. + + + + + + + + diff --git a/docs/talks/bhd2020/images/card-dmriprep.svg b/docs/talks/bhd2020/images/card-dmriprep.svg new file mode 100644 index 0000000..ce80e46 --- /dev/null +++ b/docs/talks/bhd2020/images/card-dmriprep.svg @@ -0,0 +1,880 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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protocol assessment + Deep Learning models to support higher-levelapplication, such as the deep-MRIQC, the EulerNumber Predictor, or the FaceDetector. + + + + + + + + + diff --git a/docs/talks/bhd2020/images/card-nibabel.svg b/docs/talks/bhd2020/images/card-nibabel.svg new file mode 100644 index 0000000..0f28dbd --- /dev/null +++ b/docs/talks/bhd2020/images/card-nibabel.svg @@ -0,0 +1,303 @@ + + + + + + + + image/svg+xml + + + + + + + + NiBabel + Access a cacophony ofneuroimaging file formats + Library supporting the neuroimaging dataformats (e.g., NIfTI, GIFTI, and CIFTI2). + + + + diff --git a/docs/talks/bhd2020/images/card-nipype.svg b/docs/talks/bhd2020/images/card-nipype.svg new file mode 100644 index 0000000..9efa331 --- /dev/null +++ b/docs/talks/bhd2020/images/card-nipype.svg @@ -0,0 +1,163 @@ + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + NiPype + Neuroimaging workflowsand interfaces in Python + The workflow engine supporting the execution graph and run time management (staging tasks, communication, data flow). + + + diff --git a/docs/talks/bhd2020/images/card-nitransforms.svg b/docs/talks/bhd2020/images/card-nitransforms.svg new file mode 100644 index 0000000..cfab31e --- /dev/null +++ b/docs/talks/bhd2020/images/card-nitransforms.svg @@ -0,0 +1,302 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + NiTransforms + I/O and manipulation ofspatial transforms + Library supporting the spatial transformationdata formats, and an easy-to-use interfacefor their application and manipulation. + + + + + + + + + + diff --git a/docs/talks/bhd2020/images/card-niworkflows.svg b/docs/talks/bhd2020/images/card-niworkflows.svg new file mode 100644 index 0000000..bff3225 --- /dev/null +++ b/docs/talks/bhd2020/images/card-niworkflows.svg @@ -0,0 +1,458 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + NiWorkflows + Neuroimagingprocessing commodities + Miscellaneous utilities for visualization, reporting,workflow management and fundamental workflowswith functionality shared across applications. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/talks/bhd2020/images/card-sdcflows.svg b/docs/talks/bhd2020/images/card-sdcflows.svg new file mode 100644 index 0000000..95c7623 --- /dev/null +++ b/docs/talks/bhd2020/images/card-sdcflows.svg @@ -0,0 +1,847 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + SDCFlows + Susceptibility distortioncorrection workflows + Library of tools for estimating and correctingfor susceptibility-derived distortions typicallyaffecting EPI images (d/fMRI). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/talks/bhd2020/images/card-smriprep.svg b/docs/talks/bhd2020/images/card-smriprep.svg new file mode 100644 index 0000000..534a46b --- /dev/null +++ b/docs/talks/bhd2020/images/card-smriprep.svg @@ -0,0 +1,2393 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + sMRIPrep + Structural MRI "Prep" + The NiPrep for structural (T1-weighted, and T2w)MRI scans, typically used in morphometry analysisand acquired for spatial reference of f/dMRI. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical preprocessing + + + Functional preprocessing + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Fuse & Conform + + + All T1w images are aligned and + averaged to form a 3D reference + image + + + + + + Skull-stripping + + + Atlas-based brain extraction + of the reference T1w image + + + + + + + + + + + + + + + + + + + + + T1-weighted + + + One or more T1w + images + + + T2-weighted + + + (Optional) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + time + + + TR + + + BOLD run + + + Time-series of blood-oxygen + level (BOLD) measurements + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Generate reference & brain mask + + + Specialized averaging of the time-series into one + volume and separate brain from background + + + Estimation of head-motion + + + Calculate rigid-body motion parameters that + minimize motion between time-steps + + + Slice-timing correction + + + (Optional) Infer the signal that would have been + measured if all slices were acquired simultaneously + + + Template + + + Average of + 152 subjects, + MNI space + + + INU Correction + + + Estimate and correct for + intensity nonuniformity (INU) + + + Spatial + normalization + + + Non-linear, spatial + alignment to the + brain template + + + Brain tissue + segmentation + + + Voxel-wise + classification on + tissues + + + Surface + reconstruction + + + Inner and outer + surfaces of the cortical + sheet are identified + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Alignment to T1w + reference + + + Spatial mapping between + BOLD and T1w +  coordinates + + + Susceptibility + distortion estimation + + + (Optional) Find a deformation + field to unwarp the BOLD series + + + + + + + + + Preprocessed + (native) + + + Resampling of + the BOLD series + in their original + space + + + Preprocessed + (other) + + + Resampling of + the BOLD series + in other target + spaces + + + + + + Preprocessed + (surface) + + + Resampling of the + BOLD series on the + cortical surfaces + + + Confounds + + + Collect/calculate nuisance series (e.g. motion + parameters, global signals, etc.) + + + + + + diff --git a/docs/talks/bhd2020/images/card-templateflow.svg b/docs/talks/bhd2020/images/card-templateflow.svg new file mode 100644 index 0000000..d220caf --- /dev/null +++ b/docs/talks/bhd2020/images/card-templateflow.svg @@ -0,0 +1,250 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + TemplateFlow + Access, interface, andflow across templates + An archive and a client tool to allow pro-grammatic access to neuroimaging templatesand atlases, by humans and machines. + + + + diff --git a/docs/assets/bhd2020/index.html b/docs/talks/bhd2020/index.html similarity index 100% rename from docs/assets/bhd2020/index.html rename to docs/talks/bhd2020/index.html diff --git a/docs/assets/bhd2020/presentation.md b/docs/talks/bhd2020/presentation.md similarity index 98% rename from docs/assets/bhd2020/presentation.md rename to docs/talks/bhd2020/presentation.md index 1bc70d6..11b2054 100644 --- a/docs/assets/bhd2020/presentation.md +++ b/docs/talks/bhd2020/presentation.md @@ -678,7 +678,7 @@ Finally, the paper also stresses the importance of containerizing applications t .pull-left[

- +


@@ -711,7 +711,7 @@ Finally, combining these interfaces we generate processing workflows to fulfill --- - +

@@ -724,7 +724,7 @@ Nipype helps understand (and opens windows in the black box) generating these gr --- - + ``` Python """Fix the affine of a rodent dataset, imposing 0.2x0.2x0.2 [mm].""" @@ -759,7 +759,7 @@ In the snippet, we can see how we can manipulate the orientation headers of a NI .pull-left[

- +



@@ -803,7 +803,7 @@ Finally (step 3) we generate a new image object with the structure of the refere .pull-left[

- +

@@ -877,7 +877,7 @@ Multiple cohorts are useful, for instance, in infant templates with averages at --- - +

@@ -922,7 +922,7 @@ Finally, NiWorkflows indeed offers workflows that can be used by end-user NiPrep --- - + diff --git a/docs/assets/torw2020/.gitignore b/docs/talks/torw2020/.gitignore similarity index 100% rename from docs/assets/torw2020/.gitignore rename to docs/talks/torw2020/.gitignore diff --git a/docs/assets/torw2020/assets/251439.cast b/docs/talks/torw2020/assets/251439.cast similarity index 100% rename from docs/assets/torw2020/assets/251439.cast rename to docs/talks/torw2020/assets/251439.cast diff --git a/docs/assets/torw2020/assets/anat_summary.png b/docs/talks/torw2020/assets/anat_summary.png similarity index 100% rename from docs/assets/torw2020/assets/anat_summary.png rename to docs/talks/torw2020/assets/anat_summary.png diff --git a/docs/assets/torw2020/assets/asciinema-player.css b/docs/talks/torw2020/assets/asciinema-player.css similarity index 100% rename from docs/assets/torw2020/assets/asciinema-player.css rename to docs/talks/torw2020/assets/asciinema-player.css 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