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| 1 | +package: fmriprep |
| 2 | +sections: |
| 3 | +- name: Summary |
| 4 | + reportlets: |
| 5 | + - bids: {datatype: figures, desc: summary, suffix: T1w} |
| 6 | +- name: <em>B<sub>0</sub></em> field mapping |
| 7 | + ordering: session,acquisition,run,fmapid |
| 8 | + reportlets: |
| 9 | + - bids: {datatype: figures, desc: mapped, suffix: fieldmap} |
| 10 | + caption: Inhomogeneities of the <em>B<sub>0</sub></em> field introduce (oftentimes severe) spatial distortions |
| 11 | + along the phase-encoding direction of the image. Some scanners produce a <em>B<sub>0</sub></em> |
| 12 | + mapping of the field, using Spiral Echo Imaging (SEI) or postprocessing a "phase-difference" |
| 13 | + acquisition. The plot below shows an anatomical "magnitude" reference and the corresponding |
| 14 | + fieldmap. |
| 15 | + description: Hover over the panels with the mouse pointer to also visualize the intensity of the |
| 16 | + field inhomogeneity in Hertz. |
| 17 | + static: false |
| 18 | + subtitle: "Preprocessed <em>B<sub>0</sub></em> mapping acquisition" |
| 19 | + - bids: {datatype: figures, desc: phasediff, suffix: fieldmap} |
| 20 | + caption: Inhomogeneities of the <em>B<sub>0</sub></em> field introduce (oftentimes severe) spatial distortions |
| 21 | + along the phase-encoding direction of the image. A Gradient-Recalled Echo (GRE) scheme was included for the |
| 22 | + mapping of the <em>B<sub>0</sub></em> inhomogeneities by subtracting the phase maps obtained at |
| 23 | + two subsequent echoes. The plot below shows an anatomical "magnitude" reference and the corresponding |
| 24 | + fieldmap. |
| 25 | + description: Hover over the panels with the mouse pointer to also visualize the intensity of the |
| 26 | + field inhomogeneity in Hertz. |
| 27 | + static: false |
| 28 | + subtitle: "Preprocessed mapping of phase-difference acquisition" |
| 29 | + - bids: {datatype: figures, desc: pepolar, suffix: fieldmap} |
| 30 | + caption: Inhomogeneities of the <em>B<sub>0</sub></em> field introduce (oftentimes severe) spatial distortions |
| 31 | + along the phase-encoding direction of the image. Utilizing two or more images with different |
| 32 | + phase-encoding polarities (PEPolar) or directions, it is possible to estimate the inhomogeneity |
| 33 | + of the field. The plot below shows a reference EPI (echo-planar imaging) volume generated |
| 34 | + using two or more EPI images with varying phase-encoding blips. |
| 35 | + description: Hover on the panels with the mouse pointer to also visualize the intensity of the |
| 36 | + inhomogeneity of the field in Hertz. |
| 37 | + static: false |
| 38 | + subtitle: "Preprocessed estimation with varying Phase-Encoding (PE) blips" |
| 39 | + - bids: {datatype: figures, desc: anat, suffix: fieldmap} |
| 40 | + caption: Inhomogeneities of the <em>B<sub>0</sub></em> field introduce (oftentimes severe) spatial distortions |
| 41 | + along the phase-encoding direction of the image. Utilizing an <em>anatomically-correct</em> acquisition |
| 42 | + (for instance, T1w or T2w), it is possible to estimate the inhomogeneity of the field by means of nonlinear |
| 43 | + registration. The plot below shows a reference EPI (echo-planar imaging) volume generated |
| 44 | + using two or more EPI images with the same PE encoding, after alignment to the anatomical scan. |
| 45 | + description: Hover on the panels with the mouse pointer to also visualize the intensity of the |
| 46 | + inhomogeneity of the field in Hertz. |
| 47 | + static: false |
| 48 | + subtitle: "Preprocessed estimation by nonlinear registration to an anatomical scan (“<em>fieldmap-less</em>”)" |
| 49 | + |
| 50 | +- name: Functional |
| 51 | + ordering: session,task,acquisition,ceagent,reconstruction,direction,run,echo |
| 52 | + reportlets: |
| 53 | + - bids: {datatype: figures, desc: summary, suffix: bold} |
| 54 | + - bids: {datatype: figures, desc: validation, suffix: bold} |
| 55 | + - bids: {datatype: figures, desc: fmapCoreg, suffix: bold} |
| 56 | + caption: The estimated fieldmap was aligned to the corresponding EPI reference |
| 57 | + with a rigid-registration process of the fieldmap reference image, |
| 58 | + using <code>antsRegistration</code>. |
| 59 | + Overlaid on top of the co-registration results, the final BOLD mask is represented |
| 60 | + with a red contour for reference. |
| 61 | + static: false |
| 62 | + subtitle: Alignment between the anatomical reference of the fieldmap and the target EPI |
| 63 | + - bids: {datatype: figures, desc: fieldmap, suffix: bold} |
| 64 | + caption: Estimated fieldmap, as reconstructed on the target BOLD run space to allow |
| 65 | + the assessment of its alignment with the distorted data. |
| 66 | + The anatomical reference is the fieldmap's reference moved into the target EPI's grid through |
| 67 | + the estimated transformation. |
| 68 | + In other words, this plot should be equivalent to that of the |
| 69 | + <em>Preprocessed estimation with varying Phase-Encoding (PE) blips</em> shown above in the |
| 70 | + fieldmap section. |
| 71 | + Therefore, the fieldmap should be positioned relative to the anatomical reference exactly |
| 72 | + as it is positioned in the reportlet above. |
| 73 | + static: false |
| 74 | + subtitle: "Reconstructed <em>B<sub>0</sub></em> map in the corresponding run's space (debug mode)" |
| 75 | + - bids: {datatype: figures, desc: sdc, suffix: bold} |
| 76 | + caption: Results of performing susceptibility distortion correction (SDC) on the |
| 77 | + BOLD reference image. The "distorted" image is the image that would be used to |
| 78 | + align to the anatomical reference if SDC were not applied. The "corrected" |
| 79 | + image is the image that was used. |
| 80 | + static: false |
| 81 | + subtitle: Susceptibility distortion correction |
| 82 | + - bids: {datatype: figures, desc: forcedsyn, suffix: bold} |
| 83 | + caption: The dataset contained some fieldmap information, but the argument <code>--force-syn</code> |
| 84 | + was used. The higher-priority SDC method was used. Here, we show the results |
| 85 | + of performing SyN-based SDC on the EPI for comparison. |
| 86 | + static: false |
| 87 | + subtitle: Experimental fieldmap-less susceptibility distortion correction |
| 88 | + - bids: {datatype: figures, desc: t2scomp, suffix: bold} |
| 89 | + caption: A T2* map was calculated from the echos. Here, we show the comparison |
| 90 | + of the T2* map and the BOLD reference map used for BOLD-T1w coregistration. |
| 91 | + The red contour shows the anatomical gray-matter mask resampled into BOLD space. |
| 92 | + static: false |
| 93 | + subtitle: T2* map |
| 94 | + - bids: {datatype: figures, desc: t2starhist, suffix: bold} |
| 95 | + caption: A histogram of estimated T2* values within the anatomically-derived gray-matter mask |
| 96 | + shown in the previous plot. Note that values are clipped at 100ms, so any extreme outliers will |
| 97 | + appear in the 100ms bin. |
| 98 | + static: false |
| 99 | + subtitle: T2* gray-matter values |
| 100 | + - bids: {datatype: figures, desc: coreg, suffix: bold} |
| 101 | + caption: This panel shows the alignment of the reference EPI (BOLD) image to the |
| 102 | + anatomical (T1-weighted) image. |
| 103 | + The reference EPI has been contrast enhanced and susceptibility-distortion |
| 104 | + corrected (if applicable) for improved anatomical fidelity. |
| 105 | + The anatomical image has been resampled into EPI space, as well as the |
| 106 | + anatomical white matter mask, which appears as a red contour. |
| 107 | + static: false |
| 108 | + subtitle: Alignment of functional and anatomical MRI data (coregistration) |
| 109 | + - bids: {datatype: figures, desc: rois, suffix: bold} |
| 110 | + caption: Brain mask calculated on the BOLD signal (red contour), along with the |
| 111 | + regions of interest (ROIs) used for the estimation of physiological and movement |
| 112 | + confounding components that can be then used as nuisance regressors in analysis.<br /> |
| 113 | + The <em>anatomical CompCor</em> ROI (magenta contour) is a mask combining |
| 114 | + CSF and WM (white-matter), where voxels containing a minimal partial volume |
| 115 | + of GM have been removed.<br /> |
| 116 | + The <em>temporal CompCor</em> ROI (blue contour) contains the top 2% most |
| 117 | + variable voxels within the brain mask.<br /> |
| 118 | + The <em>brain edge</em> (or <em>crown</em>) ROI (green contour) picks signals |
| 119 | + outside but close to the brain, which are decomposed into 24 principal components. |
| 120 | + subtitle: Brain mask and (anatomical/temporal) CompCor ROIs |
| 121 | + - bids: |
| 122 | + datatype: figures |
| 123 | + desc: '[at]compcor' |
| 124 | + extension: [.html] |
| 125 | + suffix: bold |
| 126 | + - bids: {datatype: figures, desc: 'compcorvar', suffix: bold} |
| 127 | + caption: The cumulative variance explained by the first k components of the |
| 128 | + <em>t/aCompCor</em> decomposition, plotted for all values of <em>k</em>. |
| 129 | + The number of components that must be included in the model in order to |
| 130 | + explain some fraction of variance in the decomposition mask can be used |
| 131 | + as a feature selection criterion for confound regression. |
| 132 | + subtitle: Variance explained by t/aCompCor components |
| 133 | + - bids: {datatype: figures, desc: carpetplot, suffix: bold} |
| 134 | + caption: Summary statistics are plotted, which may reveal trends or artifacts |
| 135 | + in the BOLD data. Global signals calculated within the whole-brain (GS), within |
| 136 | + the white-matter (WM) and within cerebro-spinal fluid (CSF) show the mean BOLD |
| 137 | + signal in their corresponding masks. DVARS and FD show the standardized DVARS |
| 138 | + and framewise-displacement measures for each time point.<br /> |
| 139 | + A carpet plot shows the time series for all voxels within the brain mask, |
| 140 | + or if <code>--cifti-output</code> was enabled, all grayordinates. |
| 141 | + See the figure legend for specific color mappings. |
| 142 | + "Ctx" = cortex, "Cb" = cerebellum, "WM" = white matter, "CSF" = cerebrospinal fluid. |
| 143 | + "d" and "s" prefixes indicate "deep" and "shallow" relative to the cortex. |
| 144 | + "Edge" indicates regions just outside the brain. |
| 145 | + subtitle: BOLD Summary |
| 146 | + - bids: {datatype: figures, desc: 'confoundcorr', suffix: bold} |
| 147 | + caption: | |
| 148 | + Left: Heatmap summarizing the correlation structure among confound variables. |
| 149 | + (Cosine bases and PCA-derived CompCor components are inherently orthogonal.) |
| 150 | + Right: magnitude of the correlation between each confound time series and the |
| 151 | + mean global signal. Strong correlations might be indicative of partial volume |
| 152 | + effects and can inform decisions about feature orthogonalization prior to |
| 153 | + confound regression. |
| 154 | + subtitle: Correlations among nuisance regressors |
| 155 | +- name: About |
| 156 | + reportlets: |
| 157 | + - bids: {datatype: figures, desc: about, suffix: T1w} |
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