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  56. </head>
    57. 

  57. <body>
    58. 

  58. 

  59. 

  60. <nav class="navbar fixed-top navbar-expand-lg navbar-light bg-light">
    61. 

  61. <div class="collapse navbar-collapse">
    62. 

  62.     <ul class="navbar-nav">
    63. 

  63.         <li class="nav-item"><a class="nav-link" href="#Summary">Summary</a></li>
    64. 

  64.         <li class="nav-item"><a class="nav-link" href="#Anatomical">Anatomical</a></li>
    65. 

  65.         <li class="nav-item dropdown">
    66. 

  66.             <a class="nav-link dropdown-toggle" id="navbarFunctional" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false" href="#">Functional</a>
    67. 

  67.             <div class="dropdown-menu" aria-labelledby="navbarFunctional">
    68. 

  68.                     <a class="dropdown-item" href="#datatype-func_desc-summary_suffix-bold_task-freerecall">Reports for: task <span class="bids-entity">freerecall</span>.</a>
    69. 

  69.                     <a class="dropdown-item" href="#datatype-func_desc-summary_suffix-bold_task-sherlockPart1">Reports for: task <span class="bids-entity">sherlockPart1</span>.</a>
    70. 

  70.                     <a class="dropdown-item" href="#datatype-func_desc-summary_suffix-bold_task-sherlockPart2">Reports for: task <span class="bids-entity">sherlockPart2</span>.</a>
    71. 

  71.             </div>
    72. 

  72.         </li>
    73. 

  73.         <li class="nav-item"><a class="nav-link" href="#About">About</a></li>
    74. 

  74.         <li class="nav-item"><a class="nav-link" href="#boilerplate">Methods</a></li>
    75. 

  75.         <li class="nav-item"><a class="nav-link" href="#errors">Errors</a></li>
    76. 

  76.     </ul>
    77. 

  77. </div>
    78. 

  78. </nav>
    79. 

  79. <noscript>
    80. 

  80.     <h1 class="text-danger"> The navigation menu uses Javascript. Without it this report might not work as expected </h1>
    81. 

  81. </noscript>
    82. 

  82. 

  83.     <div id="Summary">
    84. 

  84.     <h1 class="sub-report-title">Summary</h1>
    85. 

  85.         <div id="datatype-anat_desc-summary_suffix-T1w">
    86. 

  86.                     <ul class="elem-desc">
    87. 

  87. 		<li>Subject ID: 04</li>
    88. 

  88. 		<li>Structural images: 1 T1-weighted </li>
    89. 

  89. 		<li>Functional series: 3</li>
    90. 

  90. 		<ul class="elem-desc">
    91. 

  91. 			<li>Task: freerecall (1 run)</li>
    92. 

  92. 			<li>Task: sherlockPart1 (1 run)</li>
    93. 

  93. 			<li>Task: sherlockPart2 (1 run)</li>
    94. 

  94. 		</ul>
    95. 

  95. 		<li>Standard output spaces: MNI152NLin2009cAsym</li>
    96. 

  96. 		<li>Non-standard output spaces: </li>
    97. 

  97. 		<li>FreeSurfer reconstruction: Not run</li>
    98. 

  98. 	</ul>
    99. 

  99.         </div>
    100. 

  100.     </div>
    101. 

  101.     <div id="Anatomical">
    102. 

  102.     <h1 class="sub-report-title">Anatomical</h1>
    103. 

  103.         <div id="datatype-anat_desc-conform_extension-['.html']_suffix-T1w">
    104. 

  104.                     <h3 class="elem-title">Anatomical Conformation</h3>
    105. 

  105. 		<ul class="elem-desc">
    106. 

  106. 			<li>Input T1w images: 1</li>
    107. 

  107. 			<li>Output orientation: RAS</li>
    108. 

  108. 			<li>Output dimensions: 192x256x256</li>
    109. 

  109. 			<li>Output voxel size: 0.9mm x 0.86mm x 0.86mm</li>
    110. 

  110. 			<li>Discarded images: 0</li>
    111. 

  111. 

  112. 		</ul>
    113. 

  113.         </div>
    114. 

  114.         <div id="datatype-anat_suffix-dseg">
    115. 

  115. <h3 class="run-title">Brain mask and brain tissue segmentation of the T1w</h3><p class="elem-caption">This panel shows the template T1-weighted image (if several T1w images were found), with contours delineating the detected brain mask and brain tissue segmentations.</p>                    <img class="svg-reportlet" src="./sub-04/figures/sub-04_dseg.svg" style="width: 100%" />
    116. 

  116. </div>
    117. 

  117. <div class="elem-filename">
    118. 

  118.     Get figure file: <a href="./sub-04/figures/sub-04_dseg.svg" target="_blank">sub-04/figures/sub-04_dseg.svg</a>
    119. 

  119. </div>
    120. 

  120. 

  121.         </div>
    122. 

  122.         <div id="datatype-anat_regex_search-True_space-.*_suffix-T1w">
    123. 

  123. <h3 class="run-title">Spatial normalization of the anatomical T1w reference</h3><p class="elem-desc">Results of nonlinear alignment of the T1w reference one or more template space(s). Hover on the panels with the mouse pointer to transition between both spaces.</p><p class="elem-caption">Spatial normalization of the T1w image to the <code>MNI152NLin2009cAsym</code> template.</p>                    <object class="svg-reportlet" type="image/svg+xml" data="./sub-04/figures/sub-04_space-MNI152NLin2009cAsym_T1w.svg">
    124. 

  124. Problem loading figure sub-04/figures/sub-04_space-MNI152NLin2009cAsym_T1w.svg. If the link below works, please try reloading the report in your browser.</object>
    125. 

  125. </div>
    126. 

  126. <div class="elem-filename">
    127. 

  127.     Get figure file: <a href="./sub-04/figures/sub-04_space-MNI152NLin2009cAsym_T1w.svg" target="_blank">sub-04/figures/sub-04_space-MNI152NLin2009cAsym_T1w.svg</a>
    128. 

  128. </div>
    129. 

  129. 

  130.         </div>
    131. 

  131.     </div>
    132. 

  132.     <div id="Functional">
    133. 

  133.     <h1 class="sub-report-title">Functional</h1>
    134. 

  134.         <div id="datatype-func_desc-summary_suffix-bold_task-freerecall">
    135. 

  135. <h2 class="sub-report-group">Reports for: task <span class="bids-entity">freerecall</span>.</h2>                    <h3 class="elem-title">Summary</h3>
    136. 

  136. 		<ul class="elem-desc">
    137. 

  137. 			<li>Repetition time (TR): 1.5s</li>
    138. 

  138. 			<li>Phase-encoding (PE) direction: MISSING - Assuming Anterior-Posterior</li>
    139. 

  139. 			<li>Slice timing correction: Not applied</li>
    140. 

  140. 			<li>Susceptibility distortion correction: None</li>
    141. 

  141. 			<li>Registration: FSL <code>flirt</code> with boundary-based registration (BBR) metric - 6 dof</li>
    142. 

  142. 			<li>Confounds collected: csf, csf_derivative1, csf_power2, csf_derivative1_power2, white_matter, white_matter_derivative1, white_matter_derivative1_power2, white_matter_power2, global_signal, global_signal_derivative1, global_signal_derivative1_power2, global_signal_power2, std_dvars, dvars, framewise_displacement, t_comp_cor_00, t_comp_cor_01, t_comp_cor_02, t_comp_cor_03, t_comp_cor_04, t_comp_cor_05, t_comp_cor_06, t_comp_cor_07, t_comp_cor_08, t_comp_cor_09, t_comp_cor_10, t_comp_cor_11, t_comp_cor_12, t_comp_cor_13, a_comp_cor_00, a_comp_cor_01, a_comp_cor_02, a_comp_cor_03, a_comp_cor_04, a_comp_cor_05, a_comp_cor_06, a_comp_cor_07, a_comp_cor_08, a_comp_cor_09, a_comp_cor_10, a_comp_cor_11, a_comp_cor_12, a_comp_cor_13, a_comp_cor_14, a_comp_cor_15, a_comp_cor_16, a_comp_cor_17, a_comp_cor_18, a_comp_cor_19, a_comp_cor_20, a_comp_cor_21, a_comp_cor_22, a_comp_cor_23, a_comp_cor_24, a_comp_cor_25, a_comp_cor_26, a_comp_cor_27, a_comp_cor_28, a_comp_cor_29, a_comp_cor_30, a_comp_cor_31, a_comp_cor_32, a_comp_cor_33, a_comp_cor_34, a_comp_cor_35, a_comp_cor_36, a_comp_cor_37, a_comp_cor_38, a_comp_cor_39, a_comp_cor_40, a_comp_cor_41, a_comp_cor_42, a_comp_cor_43, a_comp_cor_44, a_comp_cor_45, a_comp_cor_46, a_comp_cor_47, a_comp_cor_48, a_comp_cor_49, a_comp_cor_50, a_comp_cor_51, a_comp_cor_52, a_comp_cor_53, a_comp_cor_54, a_comp_cor_55, a_comp_cor_56, a_comp_cor_57, a_comp_cor_58, a_comp_cor_59, a_comp_cor_60, a_comp_cor_61, a_comp_cor_62, a_comp_cor_63, a_comp_cor_64, a_comp_cor_65, a_comp_cor_66, a_comp_cor_67, a_comp_cor_68, a_comp_cor_69, a_comp_cor_70, a_comp_cor_71, a_comp_cor_72, a_comp_cor_73, a_comp_cor_74, a_comp_cor_75, a_comp_cor_76, a_comp_cor_77, a_comp_cor_78, a_comp_cor_79, a_comp_cor_80, a_comp_cor_81, a_comp_cor_82, a_comp_cor_83, a_comp_cor_84, a_comp_cor_85, a_comp_cor_86, a_comp_cor_87, a_comp_cor_88, a_comp_cor_89, a_comp_cor_90, a_comp_cor_91, a_comp_cor_92, a_comp_cor_93, a_comp_cor_94, a_comp_cor_95, a_comp_cor_96, a_comp_cor_97, a_comp_cor_98, a_comp_cor_99, a_comp_cor_100, a_comp_cor_101, a_comp_cor_102, a_comp_cor_103, a_comp_cor_104, a_comp_cor_105, a_comp_cor_106, a_comp_cor_107, a_comp_cor_108, a_comp_cor_109, a_comp_cor_110, a_comp_cor_111, a_comp_cor_112, a_comp_cor_113, a_comp_cor_114, a_comp_cor_115, a_comp_cor_116, a_comp_cor_117, a_comp_cor_118, a_comp_cor_119, a_comp_cor_120, a_comp_cor_121, a_comp_cor_122, a_comp_cor_123, a_comp_cor_124, a_comp_cor_125, a_comp_cor_126, a_comp_cor_127, a_comp_cor_128, a_comp_cor_129, a_comp_cor_130, a_comp_cor_131, a_comp_cor_132, a_comp_cor_133, a_comp_cor_134, a_comp_cor_135, a_comp_cor_136, a_comp_cor_137, a_comp_cor_138, a_comp_cor_139, a_comp_cor_140, a_comp_cor_141, a_comp_cor_142, a_comp_cor_143, a_comp_cor_144, a_comp_cor_145, a_comp_cor_146, a_comp_cor_147, a_comp_cor_148, a_comp_cor_149, a_comp_cor_150, a_comp_cor_151, a_comp_cor_152, a_comp_cor_153, a_comp_cor_154, a_comp_cor_155, a_comp_cor_156, a_comp_cor_157, a_comp_cor_158, a_comp_cor_159, a_comp_cor_160, a_comp_cor_161, a_comp_cor_162, a_comp_cor_163, a_comp_cor_164, a_comp_cor_165, a_comp_cor_166, a_comp_cor_167, a_comp_cor_168, a_comp_cor_169, a_comp_cor_170, a_comp_cor_171, a_comp_cor_172, a_comp_cor_173, a_comp_cor_174, a_comp_cor_175, a_comp_cor_176, a_comp_cor_177, a_comp_cor_178, a_comp_cor_179, a_comp_cor_180, a_comp_cor_181, a_comp_cor_182, a_comp_cor_183, a_comp_cor_184, a_comp_cor_185, a_comp_cor_186, a_comp_cor_187, a_comp_cor_188, a_comp_cor_189, a_comp_cor_190, a_comp_cor_191, a_comp_cor_192, a_comp_cor_193, a_comp_cor_194, a_comp_cor_195, a_comp_cor_196, a_comp_cor_197, a_comp_cor_198, a_comp_cor_199, a_comp_cor_200, a_comp_cor_201, a_comp_cor_202, a_comp_cor_203, a_comp_cor_204, a_comp_cor_205, a_comp_cor_206, a_comp_cor_207, a_comp_cor_208, a_comp_cor_209, a_comp_cor_210, a_comp_cor_211, a_comp_cor_212, a_comp_cor_213, a_comp_cor_214, a_comp_cor_215, a_comp_cor_216, a_comp_cor_217, a_comp_cor_218, a_comp_cor_219, a_comp_cor_220, a_comp_cor_221, a_comp_cor_222, a_comp_cor_223, a_comp_cor_224, a_comp_cor_225, a_comp_cor_226, a_comp_cor_227, a_comp_cor_228, a_comp_cor_229, a_comp_cor_230, a_comp_cor_231, a_comp_cor_232, cosine00, cosine01, cosine02, cosine03, cosine04, cosine05, cosine06, cosine07, cosine08, trans_x, trans_x_derivative1, trans_x_derivative1_power2, trans_x_power2, trans_y, trans_y_derivative1, trans_y_power2, trans_y_derivative1_power2, trans_z, trans_z_derivative1, trans_z_derivative1_power2, trans_z_power2, rot_x, rot_x_derivative1, rot_x_derivative1_power2, rot_x_power2, rot_y, rot_y_derivative1, rot_y_power2, rot_y_derivative1_power2, rot_z, rot_z_derivative1, rot_z_derivative1_power2, rot_z_power2, motion_outlier00, motion_outlier01, motion_outlier02, motion_outlier03, motion_outlier04, motion_outlier05, motion_outlier06, motion_outlier07, motion_outlier08, motion_outlier09, motion_outlier10, motion_outlier11, motion_outlier12, motion_outlier13, motion_outlier14, motion_outlier15, motion_outlier16, motion_outlier17, motion_outlier18, motion_outlier19, motion_outlier20, motion_outlier21, motion_outlier22, motion_outlier23, motion_outlier24, motion_outlier25, motion_outlier26, motion_outlier27, motion_outlier28, motion_outlier29, motion_outlier30, motion_outlier31, motion_outlier32, motion_outlier33, motion_outlier34, motion_outlier35, motion_outlier36, motion_outlier37, motion_outlier38, motion_outlier39, motion_outlier40, motion_outlier41, motion_outlier42</li>
    143. 

  143. 			<li>Non-steady-state volumes: 0</li>
    144. 

  144. 		</ul>
    145. 

  145.         </div>
    146. 

  146.         <div id="datatype-func_desc-flirtbbr_suffix-bold_task-freerecall">
    147. 

  147. <h3 class="run-title">Alignment of functional and anatomical MRI data (surface driven)</h3><p class="elem-caption">FSL <code>flirt</code> was used to generate transformations from EPI-space to T1w-space - The white matter mask calculated with FSL <code>fast</code> (brain tissue segmentation) was used for BBR. Note that Nearest Neighbor interpolation is used in the reportlets in order to highlight potential spin-history and other artifacts, whereas final images are resampled using Lanczos interpolation.</p>                    <object class="svg-reportlet" type="image/svg+xml" data="./sub-04/figures/sub-04_task-freerecall_desc-flirtbbr_bold.svg">
    148. 

  148. Problem loading figure sub-04/figures/sub-04_task-freerecall_desc-flirtbbr_bold.svg. If the link below works, please try reloading the report in your browser.</object>
    149. 

  149. </div>
    150. 

  150. <div class="elem-filename">
    151. 

  151.     Get figure file: <a href="./sub-04/figures/sub-04_task-freerecall_desc-flirtbbr_bold.svg" target="_blank">sub-04/figures/sub-04_task-freerecall_desc-flirtbbr_bold.svg</a>
    152. 

  152. </div>
    153. 

  153. 

  154.         </div>
    155. 

  155.         <div id="datatype-func_desc-rois_suffix-bold_task-freerecall">
    156. 

  156. <h3 class="run-title">Brain mask and (temporal/anatomical) CompCor ROIs</h3><p class="elem-caption">Brain mask calculated on the BOLD signal (red contour), along with the masks used for a/tCompCor.<br />The aCompCor mask (magenta contour) is a conservative CSF and white-matter mask for extracting physiological and movement confounds. <br />The fCompCor mask (blue contour) contains the top 5% most variable voxels within a heavily-eroded brain-mask.</p>                    <img class="svg-reportlet" src="./sub-04/figures/sub-04_task-freerecall_desc-rois_bold.svg" style="width: 100%" />
    157. 

  157. </div>
    158. 

  158. <div class="elem-filename">
    159. 

  159.     Get figure file: <a href="./sub-04/figures/sub-04_task-freerecall_desc-rois_bold.svg" target="_blank">sub-04/figures/sub-04_task-freerecall_desc-rois_bold.svg</a>
    160. 

  160. </div>
    161. 

  161. 

  162.         </div>
    163. 

  163.         <div id="datatype-func_desc-compcorvar_suffix-bold_task-freerecall">
    164. 

  164. <h3 class="run-title">Variance explained by t/aCompCor components</h3><p class="elem-caption">The cumulative variance explained by the first k components of the <em>t/aCompCor</em> decomposition, plotted for all values of <em>k</em>. The number of components that must be included in the model in order to explain some fraction of variance in the decomposition mask can be used as a feature selection criterion for confound regression.</p>                    <img class="svg-reportlet" src="./sub-04/figures/sub-04_task-freerecall_desc-compcorvar_bold.svg" style="width: 100%" />
    165. 

  165. </div>
    166. 

  166. <div class="elem-filename">
    167. 

  167.     Get figure file: <a href="./sub-04/figures/sub-04_task-freerecall_desc-compcorvar_bold.svg" target="_blank">sub-04/figures/sub-04_task-freerecall_desc-compcorvar_bold.svg</a>
    168. 

  168. </div>
    169. 

  169. 

  170.         </div>
    171. 

  171.         <div id="datatype-func_desc-carpetplot_suffix-bold_task-freerecall">
    172. 

  172. <h3 class="run-title">BOLD Summary</h3><p class="elem-caption">Summary statistics are plotted, which may reveal trends or artifacts in the BOLD data. Global signals calculated within the whole-brain (GS), within the white-matter (WM) and within cerebro-spinal fluid (CSF) show the mean BOLD signal in their corresponding masks. DVARS and FD show the standardized DVARS and framewise-displacement measures for each time point.<br />A carpet plot shows the time series for all voxels within the brain mask. Voxels are grouped into cortical (blue), and subcortical (orange) gray matter, cerebellum (green) and white matter and CSF (red), indicated by the color map on the left-hand side.</p>                    <img class="svg-reportlet" src="./sub-04/figures/sub-04_task-freerecall_desc-carpetplot_bold.svg" style="width: 100%" />
    173. 

  173. </div>
    174. 

  174. <div class="elem-filename">
    175. 

  175.     Get figure file: <a href="./sub-04/figures/sub-04_task-freerecall_desc-carpetplot_bold.svg" target="_blank">sub-04/figures/sub-04_task-freerecall_desc-carpetplot_bold.svg</a>
    176. 

  176. </div>
    177. 

  177. 

  178.         </div>
    179. 

  179.         <div id="datatype-func_desc-confoundcorr_suffix-bold_task-freerecall">
    180. 

  180. <h3 class="run-title">Correlations among nuisance regressors</h3><p class="elem-caption">Left: Heatmap summarizing the correlation structure among confound variables.
    181. 

  181. (Cosine bases and PCA-derived CompCor components are inherently orthogonal.)
    182. 

  182. Right: magnitude of the correlation between each confound time series and the
    183. 

  183. mean global signal. Strong correlations might be indicative of partial volume
    184. 

  184. effects and can inform decisions about feature orthogonalization prior to
    185. 

  185. confound regression.
    186. 

  186. </p>                    <img class="svg-reportlet" src="./sub-04/figures/sub-04_task-freerecall_desc-confoundcorr_bold.svg" style="width: 100%" />
    187. 

  187. </div>
    188. 

  188. <div class="elem-filename">
    189. 

  189.     Get figure file: <a href="./sub-04/figures/sub-04_task-freerecall_desc-confoundcorr_bold.svg" target="_blank">sub-04/figures/sub-04_task-freerecall_desc-confoundcorr_bold.svg</a>
    190. 

  190. </div>
    191. 

  191. 

  192.         </div>
    193. 

  193.         <div id="datatype-func_desc-summary_suffix-bold_task-sherlockPart1">
    194. 

  194. <h2 class="sub-report-group">Reports for: task <span class="bids-entity">sherlockPart1</span>.</h2>                    <h3 class="elem-title">Summary</h3>
    195. 

  195. 		<ul class="elem-desc">
    196. 

  196. 			<li>Repetition time (TR): 1.5s</li>
    197. 

  197. 			<li>Phase-encoding (PE) direction: MISSING - Assuming Anterior-Posterior</li>
    198. 

  198. 			<li>Slice timing correction: Not applied</li>
    199. 

  199. 			<li>Susceptibility distortion correction: None</li>
    200. 

  200. 			<li>Registration: FSL <code>flirt</code> with boundary-based registration (BBR) metric - 6 dof</li>
    201. 

  201. 			<li>Confounds collected: csf, csf_derivative1, csf_power2, csf_derivative1_power2, white_matter, white_matter_derivative1, white_matter_derivative1_power2, white_matter_power2, global_signal, global_signal_derivative1, global_signal_derivative1_power2, global_signal_power2, std_dvars, dvars, framewise_displacement, t_comp_cor_00, t_comp_cor_01, t_comp_cor_02, t_comp_cor_03, t_comp_cor_04, t_comp_cor_05, t_comp_cor_06, t_comp_cor_07, t_comp_cor_08, t_comp_cor_09, t_comp_cor_10, a_comp_cor_00, a_comp_cor_01, a_comp_cor_02, a_comp_cor_03, a_comp_cor_04, a_comp_cor_05, a_comp_cor_06, a_comp_cor_07, a_comp_cor_08, a_comp_cor_09, a_comp_cor_10, a_comp_cor_11, a_comp_cor_12, a_comp_cor_13, a_comp_cor_14, a_comp_cor_15, a_comp_cor_16, a_comp_cor_17, a_comp_cor_18, a_comp_cor_19, a_comp_cor_20, a_comp_cor_21, a_comp_cor_22, a_comp_cor_23, a_comp_cor_24, a_comp_cor_25, a_comp_cor_26, a_comp_cor_27, a_comp_cor_28, a_comp_cor_29, a_comp_cor_30, a_comp_cor_31, a_comp_cor_32, a_comp_cor_33, a_comp_cor_34, a_comp_cor_35, a_comp_cor_36, a_comp_cor_37, a_comp_cor_38, a_comp_cor_39, a_comp_cor_40, a_comp_cor_41, a_comp_cor_42, a_comp_cor_43, a_comp_cor_44, a_comp_cor_45, a_comp_cor_46, a_comp_cor_47, a_comp_cor_48, a_comp_cor_49, a_comp_cor_50, a_comp_cor_51, a_comp_cor_52, a_comp_cor_53, a_comp_cor_54, a_comp_cor_55, a_comp_cor_56, a_comp_cor_57, a_comp_cor_58, a_comp_cor_59, a_comp_cor_60, a_comp_cor_61, a_comp_cor_62, a_comp_cor_63, a_comp_cor_64, a_comp_cor_65, a_comp_cor_66, a_comp_cor_67, a_comp_cor_68, a_comp_cor_69, a_comp_cor_70, a_comp_cor_71, a_comp_cor_72, a_comp_cor_73, a_comp_cor_74, a_comp_cor_75, a_comp_cor_76, a_comp_cor_77, a_comp_cor_78, a_comp_cor_79, a_comp_cor_80, a_comp_cor_81, a_comp_cor_82, a_comp_cor_83, a_comp_cor_84, a_comp_cor_85, a_comp_cor_86, a_comp_cor_87, a_comp_cor_88, a_comp_cor_89, a_comp_cor_90, a_comp_cor_91, a_comp_cor_92, a_comp_cor_93, a_comp_cor_94, a_comp_cor_95, a_comp_cor_96, a_comp_cor_97, a_comp_cor_98, a_comp_cor_99, a_comp_cor_100, a_comp_cor_101, a_comp_cor_102, a_comp_cor_103, a_comp_cor_104, a_comp_cor_105, a_comp_cor_106, a_comp_cor_107, a_comp_cor_108, a_comp_cor_109, a_comp_cor_110, a_comp_cor_111, a_comp_cor_112, a_comp_cor_113, a_comp_cor_114, a_comp_cor_115, a_comp_cor_116, a_comp_cor_117, a_comp_cor_118, a_comp_cor_119, a_comp_cor_120, a_comp_cor_121, a_comp_cor_122, a_comp_cor_123, a_comp_cor_124, a_comp_cor_125, a_comp_cor_126, a_comp_cor_127, a_comp_cor_128, a_comp_cor_129, a_comp_cor_130, a_comp_cor_131, a_comp_cor_132, a_comp_cor_133, a_comp_cor_134, a_comp_cor_135, a_comp_cor_136, a_comp_cor_137, a_comp_cor_138, a_comp_cor_139, a_comp_cor_140, a_comp_cor_141, a_comp_cor_142, a_comp_cor_143, a_comp_cor_144, a_comp_cor_145, a_comp_cor_146, a_comp_cor_147, a_comp_cor_148, a_comp_cor_149, a_comp_cor_150, a_comp_cor_151, a_comp_cor_152, a_comp_cor_153, a_comp_cor_154, a_comp_cor_155, a_comp_cor_156, a_comp_cor_157, a_comp_cor_158, a_comp_cor_159, a_comp_cor_160, a_comp_cor_161, a_comp_cor_162, a_comp_cor_163, a_comp_cor_164, a_comp_cor_165, a_comp_cor_166, a_comp_cor_167, a_comp_cor_168, a_comp_cor_169, a_comp_cor_170, a_comp_cor_171, a_comp_cor_172, a_comp_cor_173, a_comp_cor_174, a_comp_cor_175, a_comp_cor_176, a_comp_cor_177, a_comp_cor_178, a_comp_cor_179, a_comp_cor_180, a_comp_cor_181, a_comp_cor_182, a_comp_cor_183, a_comp_cor_184, a_comp_cor_185, a_comp_cor_186, a_comp_cor_187, a_comp_cor_188, a_comp_cor_189, a_comp_cor_190, a_comp_cor_191, a_comp_cor_192, a_comp_cor_193, a_comp_cor_194, a_comp_cor_195, a_comp_cor_196, a_comp_cor_197, a_comp_cor_198, a_comp_cor_199, a_comp_cor_200, a_comp_cor_201, a_comp_cor_202, a_comp_cor_203, a_comp_cor_204, a_comp_cor_205, a_comp_cor_206, a_comp_cor_207, a_comp_cor_208, a_comp_cor_209, a_comp_cor_210, a_comp_cor_211, a_comp_cor_212, a_comp_cor_213, a_comp_cor_214, a_comp_cor_215, a_comp_cor_216, a_comp_cor_217, a_comp_cor_218, a_comp_cor_219, a_comp_cor_220, a_comp_cor_221, a_comp_cor_222, a_comp_cor_223, a_comp_cor_224, a_comp_cor_225, a_comp_cor_226, a_comp_cor_227, a_comp_cor_228, a_comp_cor_229, a_comp_cor_230, a_comp_cor_231, a_comp_cor_232, a_comp_cor_233, a_comp_cor_234, a_comp_cor_235, a_comp_cor_236, a_comp_cor_237, a_comp_cor_238, a_comp_cor_239, a_comp_cor_240, a_comp_cor_241, a_comp_cor_242, a_comp_cor_243, a_comp_cor_244, a_comp_cor_245, a_comp_cor_246, a_comp_cor_247, a_comp_cor_248, a_comp_cor_249, a_comp_cor_250, a_comp_cor_251, a_comp_cor_252, a_comp_cor_253, a_comp_cor_254, a_comp_cor_255, a_comp_cor_256, a_comp_cor_257, a_comp_cor_258, a_comp_cor_259, a_comp_cor_260, a_comp_cor_261, a_comp_cor_262, a_comp_cor_263, a_comp_cor_264, a_comp_cor_265, a_comp_cor_266, a_comp_cor_267, a_comp_cor_268, a_comp_cor_269, a_comp_cor_270, a_comp_cor_271, a_comp_cor_272, a_comp_cor_273, a_comp_cor_274, a_comp_cor_275, a_comp_cor_276, a_comp_cor_277, a_comp_cor_278, a_comp_cor_279, a_comp_cor_280, a_comp_cor_281, a_comp_cor_282, a_comp_cor_283, a_comp_cor_284, a_comp_cor_285, a_comp_cor_286, a_comp_cor_287, a_comp_cor_288, a_comp_cor_289, a_comp_cor_290, a_comp_cor_291, a_comp_cor_292, a_comp_cor_293, a_comp_cor_294, a_comp_cor_295, a_comp_cor_296, a_comp_cor_297, a_comp_cor_298, a_comp_cor_299, a_comp_cor_300, a_comp_cor_301, a_comp_cor_302, a_comp_cor_303, a_comp_cor_304, a_comp_cor_305, a_comp_cor_306, a_comp_cor_307, a_comp_cor_308, a_comp_cor_309, a_comp_cor_310, a_comp_cor_311, a_comp_cor_312, a_comp_cor_313, a_comp_cor_314, a_comp_cor_315, a_comp_cor_316, a_comp_cor_317, a_comp_cor_318, a_comp_cor_319, a_comp_cor_320, a_comp_cor_321, a_comp_cor_322, a_comp_cor_323, a_comp_cor_324, a_comp_cor_325, a_comp_cor_326, a_comp_cor_327, a_comp_cor_328, a_comp_cor_329, a_comp_cor_330, a_comp_cor_331, a_comp_cor_332, a_comp_cor_333, a_comp_cor_334, a_comp_cor_335, a_comp_cor_336, a_comp_cor_337, a_comp_cor_338, a_comp_cor_339, a_comp_cor_340, a_comp_cor_341, a_comp_cor_342, a_comp_cor_343, a_comp_cor_344, a_comp_cor_345, a_comp_cor_346, a_comp_cor_347, a_comp_cor_348, a_comp_cor_349, a_comp_cor_350, a_comp_cor_351, a_comp_cor_352, a_comp_cor_353, a_comp_cor_354, a_comp_cor_355, a_comp_cor_356, a_comp_cor_357, a_comp_cor_358, a_comp_cor_359, a_comp_cor_360, a_comp_cor_361, a_comp_cor_362, a_comp_cor_363, a_comp_cor_364, a_comp_cor_365, a_comp_cor_366, a_comp_cor_367, a_comp_cor_368, a_comp_cor_369, a_comp_cor_370, a_comp_cor_371, a_comp_cor_372, a_comp_cor_373, a_comp_cor_374, a_comp_cor_375, a_comp_cor_376, a_comp_cor_377, a_comp_cor_378, a_comp_cor_379, a_comp_cor_380, a_comp_cor_381, a_comp_cor_382, a_comp_cor_383, a_comp_cor_384, a_comp_cor_385, a_comp_cor_386, a_comp_cor_387, a_comp_cor_388, a_comp_cor_389, a_comp_cor_390, a_comp_cor_391, a_comp_cor_392, a_comp_cor_393, a_comp_cor_394, a_comp_cor_395, a_comp_cor_396, a_comp_cor_397, a_comp_cor_398, a_comp_cor_399, a_comp_cor_400, a_comp_cor_401, a_comp_cor_402, a_comp_cor_403, a_comp_cor_404, a_comp_cor_405, a_comp_cor_406, a_comp_cor_407, a_comp_cor_408, a_comp_cor_409, a_comp_cor_410, a_comp_cor_411, a_comp_cor_412, a_comp_cor_413, a_comp_cor_414, a_comp_cor_415, a_comp_cor_416, a_comp_cor_417, a_comp_cor_418, a_comp_cor_419, a_comp_cor_420, a_comp_cor_421, a_comp_cor_422, a_comp_cor_423, a_comp_cor_424, a_comp_cor_425, a_comp_cor_426, a_comp_cor_427, a_comp_cor_428, a_comp_cor_429, a_comp_cor_430, a_comp_cor_431, a_comp_cor_432, a_comp_cor_433, a_comp_cor_434, a_comp_cor_435, a_comp_cor_436, a_comp_cor_437, a_comp_cor_438, a_comp_cor_439, a_comp_cor_440, a_comp_cor_441, a_comp_cor_442, a_comp_cor_443, a_comp_cor_444, a_comp_cor_445, a_comp_cor_446, a_comp_cor_447, a_comp_cor_448, a_comp_cor_449, a_comp_cor_450, a_comp_cor_451, a_comp_cor_452, a_comp_cor_453, a_comp_cor_454, a_comp_cor_455, a_comp_cor_456, a_comp_cor_457, a_comp_cor_458, a_comp_cor_459, a_comp_cor_460, a_comp_cor_461, a_comp_cor_462, a_comp_cor_463, a_comp_cor_464, a_comp_cor_465, a_comp_cor_466, a_comp_cor_467, a_comp_cor_468, a_comp_cor_469, a_comp_cor_470, a_comp_cor_471, a_comp_cor_472, a_comp_cor_473, a_comp_cor_474, a_comp_cor_475, a_comp_cor_476, a_comp_cor_477, a_comp_cor_478, a_comp_cor_479, a_comp_cor_480, a_comp_cor_481, a_comp_cor_482, a_comp_cor_483, a_comp_cor_484, a_comp_cor_485, a_comp_cor_486, a_comp_cor_487, a_comp_cor_488, a_comp_cor_489, a_comp_cor_490, a_comp_cor_491, a_comp_cor_492, a_comp_cor_493, a_comp_cor_494, a_comp_cor_495, a_comp_cor_496, a_comp_cor_497, a_comp_cor_498, a_comp_cor_499, a_comp_cor_500, a_comp_cor_501, a_comp_cor_502, a_comp_cor_503, a_comp_cor_504, a_comp_cor_505, a_comp_cor_506, a_comp_cor_507, a_comp_cor_508, a_comp_cor_509, a_comp_cor_510, a_comp_cor_511, a_comp_cor_512, a_comp_cor_513, a_comp_cor_514, a_comp_cor_515, a_comp_cor_516, a_comp_cor_517, a_comp_cor_518, a_comp_cor_519, a_comp_cor_520, a_comp_cor_521, a_comp_cor_522, cosine00, cosine01, cosine02, cosine03, cosine04, cosine05, cosine06, cosine07, cosine08, cosine09, cosine10, cosine11, cosine12, cosine13, cosine14, cosine15, cosine16, cosine17, cosine18, cosine19, cosine20, trans_x, trans_x_derivative1, trans_x_derivative1_power2, trans_x_power2, trans_y, trans_y_derivative1, trans_y_power2, trans_y_derivative1_power2, trans_z, trans_z_derivative1, trans_z_derivative1_power2, trans_z_power2, rot_x, rot_x_derivative1, rot_x_derivative1_power2, rot_x_power2, rot_y, rot_y_derivative1, rot_y_power2, rot_y_derivative1_power2, rot_z, rot_z_derivative1, rot_z_derivative1_power2, rot_z_power2, motion_outlier00, motion_outlier01, motion_outlier02, motion_outlier03, motion_outlier04, motion_outlier05, motion_outlier06, motion_outlier07, motion_outlier08, motion_outlier09, motion_outlier10, motion_outlier11, motion_outlier12, motion_outlier13, motion_outlier14, motion_outlier15, motion_outlier16, motion_outlier17, motion_outlier18, motion_outlier19, motion_outlier20, motion_outlier21, motion_outlier22, motion_outlier23, motion_outlier24, motion_outlier25, motion_outlier26, motion_outlier27, motion_outlier28, motion_outlier29, motion_outlier30, motion_outlier31, motion_outlier32, motion_outlier33, motion_outlier34, motion_outlier35, motion_outlier36, motion_outlier37, motion_outlier38, motion_outlier39, motion_outlier40, motion_outlier41, motion_outlier42, motion_outlier43, motion_outlier44, motion_outlier45, motion_outlier46, motion_outlier47, motion_outlier48, motion_outlier49, motion_outlier50, motion_outlier51, motion_outlier52, motion_outlier53, motion_outlier54, motion_outlier55, motion_outlier56, motion_outlier57, motion_outlier58, motion_outlier59, motion_outlier60, motion_outlier61, motion_outlier62, motion_outlier63, motion_outlier64, motion_outlier65, motion_outlier66, motion_outlier67, motion_outlier68, motion_outlier69, motion_outlier70, motion_outlier71, motion_outlier72, motion_outlier73, motion_outlier74, motion_outlier75, motion_outlier76, motion_outlier77, motion_outlier78, motion_outlier79</li>
    202. 

  202. 			<li>Non-steady-state volumes: 0</li>
    203. 

  203. 		</ul>
    204. 

  204.         </div>
    205. 

  205.         <div id="datatype-func_desc-flirtbbr_suffix-bold_task-sherlockPart1">
    206. 

  206. <h3 class="run-title">Alignment of functional and anatomical MRI data (surface driven)</h3><p class="elem-caption">FSL <code>flirt</code> was used to generate transformations from EPI-space to T1w-space - The white matter mask calculated with FSL <code>fast</code> (brain tissue segmentation) was used for BBR. Note that Nearest Neighbor interpolation is used in the reportlets in order to highlight potential spin-history and other artifacts, whereas final images are resampled using Lanczos interpolation.</p>                    <object class="svg-reportlet" type="image/svg+xml" data="./sub-04/figures/sub-04_task-sherlockPart1_desc-flirtbbr_bold.svg">
    207. 

  207. Problem loading figure sub-04/figures/sub-04_task-sherlockPart1_desc-flirtbbr_bold.svg. If the link below works, please try reloading the report in your browser.</object>
    208. 

  208. </div>
    209. 

  209. <div class="elem-filename">
    210. 

  210.     Get figure file: <a href="./sub-04/figures/sub-04_task-sherlockPart1_desc-flirtbbr_bold.svg" target="_blank">sub-04/figures/sub-04_task-sherlockPart1_desc-flirtbbr_bold.svg</a>
    211. 

  211. </div>
    212. 

  212. 

  213.         </div>
    214. 

  214.         <div id="datatype-func_desc-rois_suffix-bold_task-sherlockPart1">
    215. 

  215. <h3 class="run-title">Brain mask and (temporal/anatomical) CompCor ROIs</h3><p class="elem-caption">Brain mask calculated on the BOLD signal (red contour), along with the masks used for a/tCompCor.<br />The aCompCor mask (magenta contour) is a conservative CSF and white-matter mask for extracting physiological and movement confounds. <br />The fCompCor mask (blue contour) contains the top 5% most variable voxels within a heavily-eroded brain-mask.</p>                    <img class="svg-reportlet" src="./sub-04/figures/sub-04_task-sherlockPart1_desc-rois_bold.svg" style="width: 100%" />
    216. 

  216. </div>
    217. 

  217. <div class="elem-filename">
    218. 

  218.     Get figure file: <a href="./sub-04/figures/sub-04_task-sherlockPart1_desc-rois_bold.svg" target="_blank">sub-04/figures/sub-04_task-sherlockPart1_desc-rois_bold.svg</a>
    219. 

  219. </div>
    220. 

  220. 

  221.         </div>
    222. 

  222.         <div id="datatype-func_desc-compcorvar_suffix-bold_task-sherlockPart1">
    223. 

  223. <h3 class="run-title">Variance explained by t/aCompCor components</h3><p class="elem-caption">The cumulative variance explained by the first k components of the <em>t/aCompCor</em> decomposition, plotted for all values of <em>k</em>. The number of components that must be included in the model in order to explain some fraction of variance in the decomposition mask can be used as a feature selection criterion for confound regression.</p>                    <img class="svg-reportlet" src="./sub-04/figures/sub-04_task-sherlockPart1_desc-compcorvar_bold.svg" style="width: 100%" />
    224. 

  224. </div>
    225. 

  225. <div class="elem-filename">
    226. 

  226.     Get figure file: <a href="./sub-04/figures/sub-04_task-sherlockPart1_desc-compcorvar_bold.svg" target="_blank">sub-04/figures/sub-04_task-sherlockPart1_desc-compcorvar_bold.svg</a>
    227. 

  227. </div>
    228. 

  228. 

  229.         </div>
    230. 

  230.         <div id="datatype-func_desc-carpetplot_suffix-bold_task-sherlockPart1">
    231. 

  231. <h3 class="run-title">BOLD Summary</h3><p class="elem-caption">Summary statistics are plotted, which may reveal trends or artifacts in the BOLD data. Global signals calculated within the whole-brain (GS), within the white-matter (WM) and within cerebro-spinal fluid (CSF) show the mean BOLD signal in their corresponding masks. DVARS and FD show the standardized DVARS and framewise-displacement measures for each time point.<br />A carpet plot shows the time series for all voxels within the brain mask. Voxels are grouped into cortical (blue), and subcortical (orange) gray matter, cerebellum (green) and white matter and CSF (red), indicated by the color map on the left-hand side.</p>                    <img class="svg-reportlet" src="./sub-04/figures/sub-04_task-sherlockPart1_desc-carpetplot_bold.svg" style="width: 100%" />
    232. 

  232. </div>
    233. 

  233. <div class="elem-filename">
    234. 

  234.     Get figure file: <a href="./sub-04/figures/sub-04_task-sherlockPart1_desc-carpetplot_bold.svg" target="_blank">sub-04/figures/sub-04_task-sherlockPart1_desc-carpetplot_bold.svg</a>
    235. 

  235. </div>
    236. 

  236. 

  237.         </div>
    238. 

  238.         <div id="datatype-func_desc-confoundcorr_suffix-bold_task-sherlockPart1">
    239. 

  239. <h3 class="run-title">Correlations among nuisance regressors</h3><p class="elem-caption">Left: Heatmap summarizing the correlation structure among confound variables.
    240. 

  240. (Cosine bases and PCA-derived CompCor components are inherently orthogonal.)
    241. 

  241. Right: magnitude of the correlation between each confound time series and the
    242. 

  242. mean global signal. Strong correlations might be indicative of partial volume
    243. 

  243. effects and can inform decisions about feature orthogonalization prior to
    244. 

  244. confound regression.
    245. 

  245. </p>                    <img class="svg-reportlet" src="./sub-04/figures/sub-04_task-sherlockPart1_desc-confoundcorr_bold.svg" style="width: 100%" />
    246. 

  246. </div>
    247. 

  247. <div class="elem-filename">
    248. 

  248.     Get figure file: <a href="./sub-04/figures/sub-04_task-sherlockPart1_desc-confoundcorr_bold.svg" target="_blank">sub-04/figures/sub-04_task-sherlockPart1_desc-confoundcorr_bold.svg</a>
    249. 

  249. </div>
    250. 

  250. 

  251.         </div>
    252. 

  252.         <div id="datatype-func_desc-summary_suffix-bold_task-sherlockPart2">
    253. 

  253. <h2 class="sub-report-group">Reports for: task <span class="bids-entity">sherlockPart2</span>.</h2>                    <h3 class="elem-title">Summary</h3>
    254. 

  254. 		<ul class="elem-desc">
    255. 

  255. 			<li>Repetition time (TR): 1.5s</li>
    256. 

  256. 			<li>Phase-encoding (PE) direction: MISSING - Assuming Anterior-Posterior</li>
    257. 

  257. 			<li>Slice timing correction: Not applied</li>
    258. 

  258. 			<li>Susceptibility distortion correction: None</li>
    259. 

  259. 			<li>Registration: FSL <code>flirt</code> with boundary-based registration (BBR) metric - 6 dof</li>
    260. 

  260. 			<li>Confounds collected: csf, csf_derivative1, csf_power2, csf_derivative1_power2, white_matter, white_matter_derivative1, white_matter_derivative1_power2, white_matter_power2, global_signal, global_signal_derivative1, global_signal_derivative1_power2, global_signal_power2, std_dvars, dvars, framewise_displacement, t_comp_cor_00, t_comp_cor_01, t_comp_cor_02, t_comp_cor_03, t_comp_cor_04, t_comp_cor_05, t_comp_cor_06, t_comp_cor_07, t_comp_cor_08, t_comp_cor_09, a_comp_cor_00, a_comp_cor_01, a_comp_cor_02, a_comp_cor_03, a_comp_cor_04, a_comp_cor_05, a_comp_cor_06, a_comp_cor_07, a_comp_cor_08, a_comp_cor_09, a_comp_cor_10, a_comp_cor_11, a_comp_cor_12, a_comp_cor_13, a_comp_cor_14, a_comp_cor_15, a_comp_cor_16, a_comp_cor_17, a_comp_cor_18, a_comp_cor_19, a_comp_cor_20, a_comp_cor_21, a_comp_cor_22, a_comp_cor_23, a_comp_cor_24, a_comp_cor_25, a_comp_cor_26, a_comp_cor_27, a_comp_cor_28, a_comp_cor_29, a_comp_cor_30, a_comp_cor_31, a_comp_cor_32, a_comp_cor_33, a_comp_cor_34, a_comp_cor_35, a_comp_cor_36, a_comp_cor_37, a_comp_cor_38, a_comp_cor_39, a_comp_cor_40, a_comp_cor_41, a_comp_cor_42, a_comp_cor_43, a_comp_cor_44, a_comp_cor_45, a_comp_cor_46, a_comp_cor_47, a_comp_cor_48, a_comp_cor_49, a_comp_cor_50, a_comp_cor_51, a_comp_cor_52, a_comp_cor_53, a_comp_cor_54, a_comp_cor_55, a_comp_cor_56, a_comp_cor_57, a_comp_cor_58, a_comp_cor_59, a_comp_cor_60, a_comp_cor_61, a_comp_cor_62, a_comp_cor_63, a_comp_cor_64, a_comp_cor_65, a_comp_cor_66, a_comp_cor_67, a_comp_cor_68, a_comp_cor_69, a_comp_cor_70, a_comp_cor_71, a_comp_cor_72, a_comp_cor_73, a_comp_cor_74, a_comp_cor_75, a_comp_cor_76, a_comp_cor_77, a_comp_cor_78, a_comp_cor_79, a_comp_cor_80, a_comp_cor_81, a_comp_cor_82, a_comp_cor_83, a_comp_cor_84, a_comp_cor_85, a_comp_cor_86, a_comp_cor_87, a_comp_cor_88, a_comp_cor_89, a_comp_cor_90, a_comp_cor_91, a_comp_cor_92, a_comp_cor_93, a_comp_cor_94, a_comp_cor_95, a_comp_cor_96, a_comp_cor_97, a_comp_cor_98, a_comp_cor_99, a_comp_cor_100, a_comp_cor_101, a_comp_cor_102, a_comp_cor_103, a_comp_cor_104, a_comp_cor_105, a_comp_cor_106, a_comp_cor_107, a_comp_cor_108, a_comp_cor_109, a_comp_cor_110, a_comp_cor_111, a_comp_cor_112, a_comp_cor_113, a_comp_cor_114, a_comp_cor_115, a_comp_cor_116, a_comp_cor_117, a_comp_cor_118, a_comp_cor_119, a_comp_cor_120, a_comp_cor_121, a_comp_cor_122, a_comp_cor_123, a_comp_cor_124, a_comp_cor_125, a_comp_cor_126, a_comp_cor_127, a_comp_cor_128, a_comp_cor_129, a_comp_cor_130, a_comp_cor_131, a_comp_cor_132, a_comp_cor_133, a_comp_cor_134, a_comp_cor_135, a_comp_cor_136, a_comp_cor_137, a_comp_cor_138, a_comp_cor_139, a_comp_cor_140, a_comp_cor_141, a_comp_cor_142, a_comp_cor_143, a_comp_cor_144, a_comp_cor_145, a_comp_cor_146, a_comp_cor_147, a_comp_cor_148, a_comp_cor_149, a_comp_cor_150, a_comp_cor_151, a_comp_cor_152, a_comp_cor_153, a_comp_cor_154, a_comp_cor_155, a_comp_cor_156, a_comp_cor_157, a_comp_cor_158, a_comp_cor_159, a_comp_cor_160, a_comp_cor_161, a_comp_cor_162, a_comp_cor_163, a_comp_cor_164, a_comp_cor_165, a_comp_cor_166, a_comp_cor_167, a_comp_cor_168, a_comp_cor_169, a_comp_cor_170, a_comp_cor_171, a_comp_cor_172, a_comp_cor_173, a_comp_cor_174, a_comp_cor_175, a_comp_cor_176, a_comp_cor_177, a_comp_cor_178, a_comp_cor_179, a_comp_cor_180, a_comp_cor_181, a_comp_cor_182, a_comp_cor_183, a_comp_cor_184, a_comp_cor_185, a_comp_cor_186, a_comp_cor_187, a_comp_cor_188, a_comp_cor_189, a_comp_cor_190, a_comp_cor_191, a_comp_cor_192, a_comp_cor_193, a_comp_cor_194, a_comp_cor_195, a_comp_cor_196, a_comp_cor_197, a_comp_cor_198, a_comp_cor_199, a_comp_cor_200, a_comp_cor_201, a_comp_cor_202, a_comp_cor_203, a_comp_cor_204, a_comp_cor_205, a_comp_cor_206, a_comp_cor_207, a_comp_cor_208, a_comp_cor_209, a_comp_cor_210, a_comp_cor_211, a_comp_cor_212, a_comp_cor_213, a_comp_cor_214, a_comp_cor_215, a_comp_cor_216, a_comp_cor_217, a_comp_cor_218, a_comp_cor_219, a_comp_cor_220, a_comp_cor_221, a_comp_cor_222, a_comp_cor_223, a_comp_cor_224, a_comp_cor_225, a_comp_cor_226, a_comp_cor_227, a_comp_cor_228, a_comp_cor_229, a_comp_cor_230, a_comp_cor_231, a_comp_cor_232, a_comp_cor_233, a_comp_cor_234, a_comp_cor_235, a_comp_cor_236, a_comp_cor_237, a_comp_cor_238, a_comp_cor_239, a_comp_cor_240, a_comp_cor_241, a_comp_cor_242, a_comp_cor_243, a_comp_cor_244, a_comp_cor_245, a_comp_cor_246, a_comp_cor_247, a_comp_cor_248, a_comp_cor_249, a_comp_cor_250, a_comp_cor_251, a_comp_cor_252, a_comp_cor_253, a_comp_cor_254, a_comp_cor_255, a_comp_cor_256, a_comp_cor_257, a_comp_cor_258, a_comp_cor_259, a_comp_cor_260, a_comp_cor_261, a_comp_cor_262, a_comp_cor_263, a_comp_cor_264, a_comp_cor_265, a_comp_cor_266, a_comp_cor_267, a_comp_cor_268, a_comp_cor_269, a_comp_cor_270, a_comp_cor_271, a_comp_cor_272, a_comp_cor_273, a_comp_cor_274, a_comp_cor_275, a_comp_cor_276, a_comp_cor_277, a_comp_cor_278, a_comp_cor_279, a_comp_cor_280, a_comp_cor_281, a_comp_cor_282, a_comp_cor_283, a_comp_cor_284, a_comp_cor_285, a_comp_cor_286, a_comp_cor_287, a_comp_cor_288, a_comp_cor_289, a_comp_cor_290, a_comp_cor_291, a_comp_cor_292, a_comp_cor_293, a_comp_cor_294, a_comp_cor_295, a_comp_cor_296, a_comp_cor_297, a_comp_cor_298, a_comp_cor_299, a_comp_cor_300, a_comp_cor_301, a_comp_cor_302, a_comp_cor_303, a_comp_cor_304, a_comp_cor_305, a_comp_cor_306, a_comp_cor_307, a_comp_cor_308, a_comp_cor_309, a_comp_cor_310, a_comp_cor_311, a_comp_cor_312, a_comp_cor_313, a_comp_cor_314, a_comp_cor_315, a_comp_cor_316, a_comp_cor_317, a_comp_cor_318, a_comp_cor_319, a_comp_cor_320, a_comp_cor_321, a_comp_cor_322, a_comp_cor_323, a_comp_cor_324, a_comp_cor_325, a_comp_cor_326, a_comp_cor_327, a_comp_cor_328, a_comp_cor_329, a_comp_cor_330, a_comp_cor_331, a_comp_cor_332, a_comp_cor_333, a_comp_cor_334, a_comp_cor_335, a_comp_cor_336, a_comp_cor_337, a_comp_cor_338, a_comp_cor_339, a_comp_cor_340, a_comp_cor_341, a_comp_cor_342, a_comp_cor_343, a_comp_cor_344, a_comp_cor_345, a_comp_cor_346, a_comp_cor_347, a_comp_cor_348, a_comp_cor_349, a_comp_cor_350, a_comp_cor_351, a_comp_cor_352, a_comp_cor_353, a_comp_cor_354, a_comp_cor_355, a_comp_cor_356, a_comp_cor_357, a_comp_cor_358, a_comp_cor_359, a_comp_cor_360, a_comp_cor_361, a_comp_cor_362, a_comp_cor_363, a_comp_cor_364, a_comp_cor_365, a_comp_cor_366, a_comp_cor_367, a_comp_cor_368, a_comp_cor_369, a_comp_cor_370, a_comp_cor_371, a_comp_cor_372, a_comp_cor_373, a_comp_cor_374, a_comp_cor_375, a_comp_cor_376, a_comp_cor_377, a_comp_cor_378, a_comp_cor_379, a_comp_cor_380, a_comp_cor_381, a_comp_cor_382, a_comp_cor_383, a_comp_cor_384, a_comp_cor_385, a_comp_cor_386, a_comp_cor_387, a_comp_cor_388, a_comp_cor_389, a_comp_cor_390, a_comp_cor_391, a_comp_cor_392, a_comp_cor_393, a_comp_cor_394, a_comp_cor_395, a_comp_cor_396, a_comp_cor_397, a_comp_cor_398, a_comp_cor_399, a_comp_cor_400, a_comp_cor_401, a_comp_cor_402, a_comp_cor_403, a_comp_cor_404, a_comp_cor_405, a_comp_cor_406, a_comp_cor_407, a_comp_cor_408, a_comp_cor_409, a_comp_cor_410, a_comp_cor_411, a_comp_cor_412, cosine00, cosine01, cosine02, cosine03, cosine04, cosine05, cosine06, cosine07, cosine08, cosine09, cosine10, cosine11, cosine12, cosine13, cosine14, cosine15, cosine16, cosine17, cosine18, cosine19, cosine20, cosine21, cosine22, trans_x, trans_x_derivative1, trans_x_derivative1_power2, trans_x_power2, trans_y, trans_y_derivative1, trans_y_power2, trans_y_derivative1_power2, trans_z, trans_z_derivative1, trans_z_derivative1_power2, trans_z_power2, rot_x, rot_x_derivative1, rot_x_derivative1_power2, rot_x_power2, rot_y, rot_y_derivative1, rot_y_power2, rot_y_derivative1_power2, rot_z, rot_z_derivative1, rot_z_derivative1_power2, rot_z_power2, motion_outlier00, motion_outlier01, motion_outlier02, motion_outlier03, motion_outlier04, motion_outlier05, motion_outlier06, motion_outlier07, motion_outlier08, motion_outlier09, motion_outlier10, motion_outlier11, motion_outlier12, motion_outlier13, motion_outlier14, motion_outlier15, motion_outlier16, motion_outlier17, motion_outlier18, motion_outlier19, motion_outlier20, motion_outlier21, motion_outlier22, motion_outlier23, motion_outlier24, motion_outlier25, motion_outlier26, motion_outlier27, motion_outlier28, motion_outlier29, motion_outlier30, motion_outlier31, motion_outlier32, motion_outlier33, motion_outlier34, motion_outlier35, motion_outlier36, motion_outlier37, motion_outlier38, motion_outlier39, motion_outlier40, motion_outlier41, motion_outlier42, motion_outlier43, motion_outlier44, motion_outlier45, motion_outlier46, motion_outlier47, motion_outlier48, motion_outlier49, motion_outlier50, motion_outlier51, motion_outlier52, motion_outlier53</li>
    261. 

  261. 			<li>Non-steady-state volumes: 0</li>
    262. 

  262. 		</ul>
    263. 

  263.         </div>
    264. 

  264.         <div id="datatype-func_desc-flirtbbr_suffix-bold_task-sherlockPart2">
    265. 

  265. <h3 class="run-title">Alignment of functional and anatomical MRI data (surface driven)</h3><p class="elem-caption">FSL <code>flirt</code> was used to generate transformations from EPI-space to T1w-space - The white matter mask calculated with FSL <code>fast</code> (brain tissue segmentation) was used for BBR. Note that Nearest Neighbor interpolation is used in the reportlets in order to highlight potential spin-history and other artifacts, whereas final images are resampled using Lanczos interpolation.</p>                    <object class="svg-reportlet" type="image/svg+xml" data="./sub-04/figures/sub-04_task-sherlockPart2_desc-flirtbbr_bold.svg">
    266. 

  266. Problem loading figure sub-04/figures/sub-04_task-sherlockPart2_desc-flirtbbr_bold.svg. If the link below works, please try reloading the report in your browser.</object>
    267. 

  267. </div>
    268. 

  268. <div class="elem-filename">
    269. 

  269.     Get figure file: <a href="./sub-04/figures/sub-04_task-sherlockPart2_desc-flirtbbr_bold.svg" target="_blank">sub-04/figures/sub-04_task-sherlockPart2_desc-flirtbbr_bold.svg</a>
    270. 

  270. </div>
    271. 

  271. 

  272.         </div>
    273. 

  273.         <div id="datatype-func_desc-rois_suffix-bold_task-sherlockPart2">
    274. 

  274. <h3 class="run-title">Brain mask and (temporal/anatomical) CompCor ROIs</h3><p class="elem-caption">Brain mask calculated on the BOLD signal (red contour), along with the masks used for a/tCompCor.<br />The aCompCor mask (magenta contour) is a conservative CSF and white-matter mask for extracting physiological and movement confounds. <br />The fCompCor mask (blue contour) contains the top 5% most variable voxels within a heavily-eroded brain-mask.</p>                    <img class="svg-reportlet" src="./sub-04/figures/sub-04_task-sherlockPart2_desc-rois_bold.svg" style="width: 100%" />
    275. 

  275. </div>
    276. 

  276. <div class="elem-filename">
    277. 

  277.     Get figure file: <a href="./sub-04/figures/sub-04_task-sherlockPart2_desc-rois_bold.svg" target="_blank">sub-04/figures/sub-04_task-sherlockPart2_desc-rois_bold.svg</a>
    278. 

  278. </div>
    279. 

  279. 

  280.         </div>
    281. 

  281.         <div id="datatype-func_desc-compcorvar_suffix-bold_task-sherlockPart2">
    282. 

  282. <h3 class="run-title">Variance explained by t/aCompCor components</h3><p class="elem-caption">The cumulative variance explained by the first k components of the <em>t/aCompCor</em> decomposition, plotted for all values of <em>k</em>. The number of components that must be included in the model in order to explain some fraction of variance in the decomposition mask can be used as a feature selection criterion for confound regression.</p>                    <img class="svg-reportlet" src="./sub-04/figures/sub-04_task-sherlockPart2_desc-compcorvar_bold.svg" style="width: 100%" />
    283. 

  283. </div>
    284. 

  284. <div class="elem-filename">
    285. 

  285.     Get figure file: <a href="./sub-04/figures/sub-04_task-sherlockPart2_desc-compcorvar_bold.svg" target="_blank">sub-04/figures/sub-04_task-sherlockPart2_desc-compcorvar_bold.svg</a>
    286. 

  286. </div>
    287. 

  287. 

  288.         </div>
    289. 

  289.         <div id="datatype-func_desc-carpetplot_suffix-bold_task-sherlockPart2">
    290. 

  290. <h3 class="run-title">BOLD Summary</h3><p class="elem-caption">Summary statistics are plotted, which may reveal trends or artifacts in the BOLD data. Global signals calculated within the whole-brain (GS), within the white-matter (WM) and within cerebro-spinal fluid (CSF) show the mean BOLD signal in their corresponding masks. DVARS and FD show the standardized DVARS and framewise-displacement measures for each time point.<br />A carpet plot shows the time series for all voxels within the brain mask. Voxels are grouped into cortical (blue), and subcortical (orange) gray matter, cerebellum (green) and white matter and CSF (red), indicated by the color map on the left-hand side.</p>                    <img class="svg-reportlet" src="./sub-04/figures/sub-04_task-sherlockPart2_desc-carpetplot_bold.svg" style="width: 100%" />
    291. 

  291. </div>
    292. 

  292. <div class="elem-filename">
    293. 

  293.     Get figure file: <a href="./sub-04/figures/sub-04_task-sherlockPart2_desc-carpetplot_bold.svg" target="_blank">sub-04/figures/sub-04_task-sherlockPart2_desc-carpetplot_bold.svg</a>
    294. 

  294. </div>
    295. 

  295. 

  296.         </div>
    297. 

  297.         <div id="datatype-func_desc-confoundcorr_suffix-bold_task-sherlockPart2">
    298. 

  298. <h3 class="run-title">Correlations among nuisance regressors</h3><p class="elem-caption">Left: Heatmap summarizing the correlation structure among confound variables.
    299. 

  299. (Cosine bases and PCA-derived CompCor components are inherently orthogonal.)
    300. 

  300. Right: magnitude of the correlation between each confound time series and the
    301. 

  301. mean global signal. Strong correlations might be indicative of partial volume
    302. 

  302. effects and can inform decisions about feature orthogonalization prior to
    303. 

  303. confound regression.
    304. 

  304. </p>                    <img class="svg-reportlet" src="./sub-04/figures/sub-04_task-sherlockPart2_desc-confoundcorr_bold.svg" style="width: 100%" />
    305. 

  305. </div>
    306. 

  306. <div class="elem-filename">
    307. 

  307.     Get figure file: <a href="./sub-04/figures/sub-04_task-sherlockPart2_desc-confoundcorr_bold.svg" target="_blank">sub-04/figures/sub-04_task-sherlockPart2_desc-confoundcorr_bold.svg</a>
    308. 

  308. </div>
    309. 

  309. 

  310.         </div>
    311. 

  311.     </div>
    312. 

  312.     <div id="About">
    313. 

  313.     <h1 class="sub-report-title">About</h1>
    314. 

  314.         <div id="datatype-anat_desc-about_suffix-T1w">
    315. 

  315.                     <ul>
    316. 

  316. 		<li>fMRIPrep version: 20.0.6</li>
    317. 

  317. 		<li>fMRIPrep command: <code>/usr/local/miniconda/bin/fmriprep /dartfs/rc/lab/D/DBIC/cosanlab/datax/Projects/sherlock /dartfs/rc/lab/D/DBIC/cosanlab/datax/Projects/sherlock/derivatives participant --participant-label sub-04 -w /work --nthreads 16 --omp-nthreads 16 --fs-license-file /dartfs/rc/lab/D/DBIC/cosanlab/datax/Resources/fmriprep/license.txt --write-graph --fs-no-reconall --notrack</code></li>
    318. 

  318. 		<li>Date preprocessed: 2020-05-18 23:33:31 -0400</li>
    319. 

  319. 	</ul>
    320. 

  320. </div>
    321. 

  321.         </div>
    322. 

  322.     </div>
    323. 

  323. 

  324. <div id="boilerplate">
    325. 

  325.     <h1 class="sub-report-title">Methods</h1>
    326. 

  326.     <p>We kindly ask to report results preprocessed with this tool using the following
    327. 

  327.        boilerplate.</p>
    328. 

  328.     <ul class="nav nav-tabs" id="myTab" role="tablist">
    329. 

  329.         <li class="nav-item">
    330. 

  330.             <a class="nav-link active" id="HTML-tab" data-toggle="tab" href="#HTML" role="tab" aria-controls="HTML" aria-selected="true">HTML</a>
    331. 

  331.         </li>
    332. 

  332.         <li class="nav-item">
    333. 

  333.             <a class="nav-link " id="Markdown-tab" data-toggle="tab" href="#Markdown" role="tab" aria-controls="Markdown" aria-selected="false">Markdown</a>
    334. 

  334.         </li>
    335. 

  335.         <li class="nav-item">
    336. 

  336.             <a class="nav-link " id="LaTeX-tab" data-toggle="tab" href="#LaTeX" role="tab" aria-controls="LaTeX" aria-selected="false">LaTeX</a>
    337. 

  337.         </li>
    338. 

  338.     </ul>
    339. 

  339.     <div class="tab-content" id="myTabContent">
    340. 

  340.       <div class="tab-pane fade active show" id="HTML" role="tabpanel" aria-labelledby="HTML-tab"><div class="boiler-html"><p>Results included in this manuscript come from preprocessing performed using <em>fMRIPrep</em> 20.0.6 (<span class="citation" data-cites="fmriprep1">Esteban, Markiewicz, et al. (2018)</span>; <span class="citation" data-cites="fmriprep2">Esteban, Blair, et al. (2018)</span>; RRID:SCR_016216), which is based on <em>Nipype</em> 1.4.2 (<span class="citation" data-cites="nipype1">Gorgolewski et al. (2011)</span>; <span class="citation" data-cites="nipype2">Gorgolewski et al. (2018)</span>; RRID:SCR_002502).</p>
    341. 

  341. <dl>
    342. 

  342. <dt>Anatomical data preprocessing</dt>
    343. 

  343. <dd><p>The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU) with <code>N4BiasFieldCorrection</code> <span class="citation" data-cites="n4">(Tustison et al. 2010)</span>, distributed with ANTs 2.2.0 <span class="citation" data-cites="ants">(Avants et al. 2008, RRID:SCR_004757)</span>, and used as T1w-reference throughout the workflow. The T1w-reference was then skull-stripped with a <em>Nipype</em> implementation of the <code>antsBrainExtraction.sh</code> workflow (from ANTs), using OASIS30ANTs as target template. Brain tissue segmentation of cerebrospinal fluid (CSF), white-matter (WM) and gray-matter (GM) was performed on the brain-extracted T1w using <code>fast</code> <span class="citation" data-cites="fsl_fast">(FSL 5.0.9, RRID:SCR_002823, Zhang, Brady, and Smith 2001)</span>. Volume-based spatial normalization to one standard space (MNI152NLin2009cAsym) was performed through nonlinear registration with <code>antsRegistration</code> (ANTs 2.2.0), using brain-extracted versions of both T1w reference and the T1w template. The following template was selected for spatial normalization: <em>ICBM 152 Nonlinear Asymmetrical template version 2009c</em> [<span class="citation" data-cites="mni152nlin2009casym">Fonov et al. (2009)</span>, RRID:SCR_008796; TemplateFlow ID: MNI152NLin2009cAsym],</p>
    344. 

  344. </dd>
    345. 

  345. <dt>Functional data preprocessing</dt>
    346. 

  346. <dd><p>For each of the 3 BOLD runs found per subject (across all tasks and sessions), the following preprocessing was performed. First, a reference volume and its skull-stripped version were generated using a custom methodology of <em>fMRIPrep</em>. Susceptibility distortion correction (SDC) was omitted. The BOLD reference was then co-registered to the T1w reference using <code>flirt</code> <span class="citation" data-cites="flirt">(FSL 5.0.9, Jenkinson and Smith 2001)</span> with the boundary-based registration <span class="citation" data-cites="bbr">(Greve and Fischl 2009)</span> cost-function. Co-registration was configured with nine degrees of freedom to account for distortions remaining in the BOLD reference. Head-motion parameters with respect to the BOLD reference (transformation matrices, and six corresponding rotation and translation parameters) are estimated before any spatiotemporal filtering using <code>mcflirt</code> <span class="citation" data-cites="mcflirt">(FSL 5.0.9, Jenkinson et al. 2002)</span>. The BOLD time-series (including slice-timing correction when applied) were resampled onto their original, native space by applying the transforms to correct for head-motion. These resampled BOLD time-series will be referred to as <em>preprocessed BOLD in original space</em>, or just <em>preprocessed BOLD</em>. The BOLD time-series were resampled into standard space, generating a <em>preprocessed BOLD run in MNI152NLin2009cAsym space</em>. First, a reference volume and its skull-stripped version were generated using a custom methodology of <em>fMRIPrep</em>. Several confounding time-series were calculated based on the <em>preprocessed BOLD</em>: framewise displacement (FD), DVARS and three region-wise global signals. FD and DVARS are calculated for each functional run, both using their implementations in <em>Nipype</em> <span class="citation" data-cites="power_fd_dvars">(following the definitions by Power et al. 2014)</span>. The three global signals are extracted within the CSF, the WM, and the whole-brain masks. Additionally, a set of physiological regressors were extracted to allow for component-based noise correction <span class="citation" data-cites="compcor">(<em>CompCor</em>, Behzadi et al. 2007)</span>. Principal components are estimated after high-pass filtering the <em>preprocessed BOLD</em> time-series (using a discrete cosine filter with 128s cut-off) for the two <em>CompCor</em> variants: temporal (tCompCor) and anatomical (aCompCor). tCompCor components are then calculated from the top 5% variable voxels within a mask covering the subcortical regions. This subcortical mask is obtained by heavily eroding the brain mask, which ensures it does not include cortical GM regions. For aCompCor, components are calculated within the intersection of the aforementioned mask and the union of CSF and WM masks calculated in T1w space, after their projection to the native space of each functional run (using the inverse BOLD-to-T1w transformation). Components are also calculated separately within the WM and CSF masks. For each CompCor decomposition, the <em>k</em> components with the largest singular values are retained, such that the retained components’ time series are sufficient to explain 50 percent of variance across the nuisance mask (CSF, WM, combined, or temporal). The remaining components are dropped from consideration. The head-motion estimates calculated in the correction step were also placed within the corresponding confounds file. The confound time series derived from head motion estimates and global signals were expanded with the inclusion of temporal derivatives and quadratic terms for each <span class="citation" data-cites="confounds_satterthwaite_2013">(Satterthwaite et al. 2013)</span>. Frames that exceeded a threshold of 0.5 mm FD or 1.5 standardised DVARS were annotated as motion outliers. All resamplings can be performed with <em>a single interpolation step</em> by composing all the pertinent transformations (i.e. head-motion transform matrices, susceptibility distortion correction when available, and co-registrations to anatomical and output spaces). Gridded (volumetric) resamplings were performed using <code>antsApplyTransforms</code> (ANTs), configured with Lanczos interpolation to minimize the smoothing effects of other kernels <span class="citation" data-cites="lanczos">(Lanczos 1964)</span>. Non-gridded (surface) resamplings were performed using <code>mri_vol2surf</code> (FreeSurfer).</p>
    347. 

  347. </dd>
    348. 

  348. </dl>
    349. 

  349. <p>Many internal operations of <em>fMRIPrep</em> use <em>Nilearn</em> 0.6.2 <span class="citation" data-cites="nilearn">(Abraham et al. 2014, RRID:SCR_001362)</span>, mostly within the functional processing workflow. For more details of the pipeline, see <a href="https://fmriprep.readthedocs.io/en/latest/workflows.html" title="FMRIPrep&#39;s documentation">the section corresponding to workflows in <em>fMRIPrep</em>’s documentation</a>.</p>
    350. 

  350. <h3 id="copyright-waiver">Copyright Waiver</h3>
    351. 

  351. <p>The above boilerplate text was automatically generated by fMRIPrep with the express intention that users should copy and paste this text into their manuscripts <em>unchanged</em>. It is released under the <a href="https://creativecommons.org/publicdomain/zero/1.0/">CC0</a> license.</p>
    352. 

  352. <h3 id="references" class="unnumbered">References</h3>
    353. 

  353. <div id="refs" class="references">
    354. 

  354. <div id="ref-nilearn">
    355. 

  355. <p>Abraham, Alexandre, Fabian Pedregosa, Michael Eickenberg, Philippe Gervais, Andreas Mueller, Jean Kossaifi, Alexandre Gramfort, Bertrand Thirion, and Gael Varoquaux. 2014. “Machine Learning for Neuroimaging with Scikit-Learn.” <em>Frontiers in Neuroinformatics</em> 8. <a href="https://doi.org/10.3389/fninf.2014.00014" class="uri">https://doi.org/10.3389/fninf.2014.00014</a>.</p>
    356. 

  356. </div>
    357. 

  357. <div id="ref-ants">
    358. 

  358. <p>Avants, B.B., C.L. Epstein, M. Grossman, and J.C. Gee. 2008. “Symmetric Diffeomorphic Image Registration with Cross-Correlation: Evaluating Automated Labeling of Elderly and Neurodegenerative Brain.” <em>Medical Image Analysis</em> 12 (1): 26–41. <a href="https://doi.org/10.1016/j.media.2007.06.004" class="uri">https://doi.org/10.1016/j.media.2007.06.004</a>.</p>
    359. 

  359. </div>
    360. 

  360. <div id="ref-compcor">
    361. 

  361. <p>Behzadi, Yashar, Khaled Restom, Joy Liau, and Thomas T. Liu. 2007. “A Component Based Noise Correction Method (CompCor) for BOLD and Perfusion Based fMRI.” <em>NeuroImage</em> 37 (1): 90–101. <a href="https://doi.org/10.1016/j.neuroimage.2007.04.042" class="uri">https://doi.org/10.1016/j.neuroimage.2007.04.042</a>.</p>
    362. 

  362. </div>
    363. 

  363. <div id="ref-fmriprep2">
    364. 

  364. <p>Esteban, Oscar, Ross Blair, Christopher J. Markiewicz, Shoshana L. Berleant, Craig Moodie, Feilong Ma, Ayse Ilkay Isik, et al. 2018. “FMRIPrep.” <em>Software</em>. Zenodo. <a href="https://doi.org/10.5281/zenodo.852659" class="uri">https://doi.org/10.5281/zenodo.852659</a>.</p>
    365. 

  365. </div>
    366. 

  366. <div id="ref-fmriprep1">
    367. 

  367. <p>Esteban, Oscar, Christopher Markiewicz, Ross W Blair, Craig Moodie, Ayse Ilkay Isik, Asier Erramuzpe Aliaga, James Kent, et al. 2018. “fMRIPrep: A Robust Preprocessing Pipeline for Functional MRI.” <em>Nature Methods</em>. <a href="https://doi.org/10.1038/s41592-018-0235-4" class="uri">https://doi.org/10.1038/s41592-018-0235-4</a>.</p>
    368. 

  368. </div>
    369. 

  369. <div id="ref-mni152nlin2009casym">
    370. 

  370. <p>Fonov, VS, AC Evans, RC McKinstry, CR Almli, and DL Collins. 2009. “Unbiased Nonlinear Average Age-Appropriate Brain Templates from Birth to Adulthood.” <em>NeuroImage</em> 47, Supplement 1: S102. <a href="https://doi.org/10.1016/S1053-8119(09)70884-5" class="uri">https://doi.org/10.1016/S1053-8119(09)70884-5</a>.</p>
    371. 

  371. </div>
    372. 

  372. <div id="ref-nipype1">
    373. 

  373. <p>Gorgolewski, K., C. D. Burns, C. Madison, D. Clark, Y. O. Halchenko, M. L. Waskom, and S. Ghosh. 2011. “Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python.” <em>Frontiers in Neuroinformatics</em> 5: 13. <a href="https://doi.org/10.3389/fninf.2011.00013" class="uri">https://doi.org/10.3389/fninf.2011.00013</a>.</p>
    374. 

  374. </div>
    375. 

  375. <div id="ref-nipype2">
    376. 

  376. <p>Gorgolewski, Krzysztof J., Oscar Esteban, Christopher J. Markiewicz, Erik Ziegler, David Gage Ellis, Michael Philipp Notter, Dorota Jarecka, et al. 2018. “Nipype.” <em>Software</em>. Zenodo. <a href="https://doi.org/10.5281/zenodo.596855" class="uri">https://doi.org/10.5281/zenodo.596855</a>.</p>
    377. 

  377. </div>
    378. 

  378. <div id="ref-bbr">
    379. 

  379. <p>Greve, Douglas N, and Bruce Fischl. 2009. “Accurate and Robust Brain Image Alignment Using Boundary-Based Registration.” <em>NeuroImage</em> 48 (1): 63–72. <a href="https://doi.org/10.1016/j.neuroimage.2009.06.060" class="uri">https://doi.org/10.1016/j.neuroimage.2009.06.060</a>.</p>
    380. 

  380. </div>
    381. 

  381. <div id="ref-mcflirt">
    382. 

  382. <p>Jenkinson, Mark, Peter Bannister, Michael Brady, and Stephen Smith. 2002. “Improved Optimization for the Robust and Accurate Linear Registration and Motion Correction of Brain Images.” <em>NeuroImage</em> 17 (2): 825–41. <a href="https://doi.org/10.1006/nimg.2002.1132" class="uri">https://doi.org/10.1006/nimg.2002.1132</a>.</p>
    383. 

  383. </div>
    384. 

  384. <div id="ref-flirt">
    385. 

  385. <p>Jenkinson, Mark, and Stephen Smith. 2001. “A Global Optimisation Method for Robust Affine Registration of Brain Images.” <em>Medical Image Analysis</em> 5 (2): 143–56. <a href="https://doi.org/10.1016/S1361-8415(01)00036-6" class="uri">https://doi.org/10.1016/S1361-8415(01)00036-6</a>.</p>
    386. 

  386. </div>
    387. 

  387. <div id="ref-lanczos">
    388. 

  388. <p>Lanczos, C. 1964. “Evaluation of Noisy Data.” <em>Journal of the Society for Industrial and Applied Mathematics Series B Numerical Analysis</em> 1 (1): 76–85. <a href="https://doi.org/10.1137/0701007" class="uri">https://doi.org/10.1137/0701007</a>.</p>
    389. 

  389. </div>
    390. 

  390. <div id="ref-power_fd_dvars">
    391. 

  391. <p>Power, Jonathan D., Anish Mitra, Timothy O. Laumann, Abraham Z. Snyder, Bradley L. Schlaggar, and Steven E. Petersen. 2014. “Methods to Detect, Characterize, and Remove Motion Artifact in Resting State fMRI.” <em>NeuroImage</em> 84 (Supplement C): 320–41. <a href="https://doi.org/10.1016/j.neuroimage.2013.08.048" class="uri">https://doi.org/10.1016/j.neuroimage.2013.08.048</a>.</p>
    392. 

  392. </div>
    393. 

  393. <div id="ref-confounds_satterthwaite_2013">
    394. 

  394. <p>Satterthwaite, Theodore D., Mark A. Elliott, Raphael T. Gerraty, Kosha Ruparel, James Loughead, Monica E. Calkins, Simon B. Eickhoff, et al. 2013. “An improved framework for confound regression and filtering for control of motion artifact in the preprocessing of resting-state functional connectivity data.” <em>NeuroImage</em> 64 (1): 240–56. <a href="https://doi.org/10.1016/j.neuroimage.2012.08.052" class="uri">https://doi.org/10.1016/j.neuroimage.2012.08.052</a>.</p>
    395. 

  395. </div>
    396. 

  396. <div id="ref-n4">
    397. 

  397. <p>Tustison, N. J., B. B. Avants, P. A. Cook, Y. Zheng, A. Egan, P. A. Yushkevich, and J. C. Gee. 2010. “N4ITK: Improved N3 Bias Correction.” <em>IEEE Transactions on Medical Imaging</em> 29 (6): 1310–20. <a href="https://doi.org/10.1109/TMI.2010.2046908" class="uri">https://doi.org/10.1109/TMI.2010.2046908</a>.</p>
    398. 

  398. </div>
    399. 

  399. <div id="ref-fsl_fast">
    400. 

  400. <p>Zhang, Y., M. Brady, and S. Smith. 2001. “Segmentation of Brain MR Images Through a Hidden Markov Random Field Model and the Expectation-Maximization Algorithm.” <em>IEEE Transactions on Medical Imaging</em> 20 (1): 45–57. <a href="https://doi.org/10.1109/42.906424" class="uri">https://doi.org/10.1109/42.906424</a>.</p>
    401. 

  401. </div>
    402. 

  402. </div></div></div>
    403. 

  403.       <div class="tab-pane fade " id="Markdown" role="tabpanel" aria-labelledby="Markdown-tab"><pre>
    404. 

  404. Results included in this manuscript come from preprocessing
    405. 

  405. performed using *fMRIPrep* 20.0.6
    406. 

  406. (@fmriprep1; @fmriprep2; RRID:SCR_016216),
    407. 

  407. which is based on *Nipype* 1.4.2
    408. 

  408. (@nipype1; @nipype2; RRID:SCR_002502).
    409. 

  409. 

  410. Anatomical data preprocessing
    411. 

  411. 

  412. : The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU)
    413. 

  413. with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.2.0 [@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow.
    414. 

  414. The T1w-reference was then skull-stripped with a *Nipype* implementation of
    415. 

  415. the `antsBrainExtraction.sh` workflow (from ANTs), using OASIS30ANTs
    416. 

  416. as target template.
    417. 

  417. Brain tissue segmentation of cerebrospinal fluid (CSF),
    418. 

  418. white-matter (WM) and gray-matter (GM) was performed on
    419. 

  419. the brain-extracted T1w using `fast` [FSL 5.0.9, RRID:SCR_002823,
    420. 

  420. @fsl_fast].
    421. 

  421. Volume-based spatial normalization to one standard space (MNI152NLin2009cAsym) was performed through
    422. 

  422. nonlinear registration with `antsRegistration` (ANTs 2.2.0),
    423. 

  423. using brain-extracted versions of both T1w reference and the T1w template.
    424. 

  424. The following template was selected for spatial normalization:
    425. 

  425. *ICBM 152 Nonlinear Asymmetrical template version 2009c* [@mni152nlin2009casym, RRID:SCR_008796; TemplateFlow ID: MNI152NLin2009cAsym], 
    426. 

  426. 

  427. Functional data preprocessing
    428. 

  428. 

  429. : For each of the 3 BOLD runs found per subject (across all
    430. 

  430. tasks and sessions), the following preprocessing was performed.
    431. 

  431. First, a reference volume and its skull-stripped version were generated
    432. 

  432. using a custom methodology of *fMRIPrep*.
    433. 

  433. Susceptibility distortion correction (SDC) was omitted.
    434. 

  434. The BOLD reference was then co-registered to the T1w reference using
    435. 

  435. `flirt` [FSL 5.0.9, @flirt] with the boundary-based registration [@bbr]
    436. 

  436. cost-function.
    437. 

  437. Co-registration was configured with nine degrees of freedom to account
    438. 

  438. for distortions remaining in the BOLD reference.
    439. 

  439. Head-motion parameters with respect to the BOLD reference
    440. 

  440. (transformation matrices, and six corresponding rotation and translation
    441. 

  441. parameters) are estimated before any spatiotemporal filtering using
    442. 

  442. `mcflirt` [FSL 5.0.9, @mcflirt].
    443. 

  443. The BOLD time-series (including slice-timing correction when applied)
    444. 

  444. were resampled onto their original, native space by applying
    445. 

  445. the transforms to correct for head-motion.
    446. 

  446. These resampled BOLD time-series will be referred to as *preprocessed
    447. 

  447. BOLD in original space*, or just *preprocessed BOLD*.
    448. 

  448. The BOLD time-series were resampled into standard space,
    449. 

  449. generating a *preprocessed BOLD run in MNI152NLin2009cAsym space*.
    450. 

  450. First, a reference volume and its skull-stripped version were generated
    451. 

  451. using a custom methodology of *fMRIPrep*.
    452. 

  452. Several confounding time-series were calculated based on the
    453. 

  453. *preprocessed BOLD*: framewise displacement (FD), DVARS and
    454. 

  454. three region-wise global signals.
    455. 

  455. FD and DVARS are calculated for each functional run, both using their
    456. 

  456. implementations in *Nipype* [following the definitions by @power_fd_dvars].
    457. 

  457. The three global signals are extracted within the CSF, the WM, and
    458. 

  458. the whole-brain masks.
    459. 

  459. Additionally, a set of physiological regressors were extracted to
    460. 

  460. allow for component-based noise correction [*CompCor*, @compcor].
    461. 

  461. Principal components are estimated after high-pass filtering the
    462. 

  462. *preprocessed BOLD* time-series (using a discrete cosine filter with
    463. 

  463. 128s cut-off) for the two *CompCor* variants: temporal (tCompCor)
    464. 

  464. and anatomical (aCompCor).
    465. 

  465. tCompCor components are then calculated from the top 5% variable
    466. 

  466. voxels within a mask covering the subcortical regions.
    467. 

  467. This subcortical mask is obtained by heavily eroding the brain mask,
    468. 

  468. which ensures it does not include cortical GM regions.
    469. 

  469. For aCompCor, components are calculated within the intersection of
    470. 

  470. the aforementioned mask and the union of CSF and WM masks calculated
    471. 

  471. in T1w space, after their projection to the native space of each
    472. 

  472. functional run (using the inverse BOLD-to-T1w transformation). Components
    473. 

  473. are also calculated separately within the WM and CSF masks.
    474. 

  474. For each CompCor decomposition, the *k* components with the largest singular
    475. 

  475. values are retained, such that the retained components' time series are
    476. 

  476. sufficient to explain 50 percent of variance across the nuisance mask (CSF,
    477. 

  477. WM, combined, or temporal). The remaining components are dropped from
    478. 

  478. consideration.
    479. 

  479. The head-motion estimates calculated in the correction step were also
    480. 

  480. placed within the corresponding confounds file.
    481. 

  481. The confound time series derived from head motion estimates and global
    482. 

  482. signals were expanded with the inclusion of temporal derivatives and
    483. 

  483. quadratic terms for each [@confounds_satterthwaite_2013].
    484. 

  484. Frames that exceeded a threshold of 0.5 mm FD or 1.5 standardised DVARS
    485. 

  485. were annotated as motion outliers.
    486. 

  486. All resamplings can be performed with *a single interpolation
    487. 

  487. step* by composing all the pertinent transformations (i.e. head-motion
    488. 

  488. transform matrices, susceptibility distortion correction when available,
    489. 

  489. and co-registrations to anatomical and output spaces).
    490. 

  490. Gridded (volumetric) resamplings were performed using `antsApplyTransforms` (ANTs),
    491. 

  491. configured with Lanczos interpolation to minimize the smoothing
    492. 

  492. effects of other kernels [@lanczos].
    493. 

  493. Non-gridded (surface) resamplings were performed using `mri_vol2surf`
    494. 

  494. (FreeSurfer).
    495. 

  495. 

  496. 

  497. Many internal operations of *fMRIPrep* use
    498. 

  498. *Nilearn* 0.6.2 [@nilearn, RRID:SCR_001362],
    499. 

  499. mostly within the functional processing workflow.
    500. 

  500. For more details of the pipeline, see [the section corresponding
    501. 

  501. to workflows in *fMRIPrep*'s documentation](https://fmriprep.readthedocs.io/en/latest/workflows.html "FMRIPrep's documentation").
    502. 

  502. 

  503. 

  504. ### Copyright Waiver
    505. 

  505. 

  506. The above boilerplate text was automatically generated by fMRIPrep
    507. 

  507. with the express intention that users should copy and paste this
    508. 

  508. text into their manuscripts *unchanged*.
    509. 

  509. It is released under the [CC0](https://creativecommons.org/publicdomain/zero/1.0/) license.
    510. 

  510. 

  511. ### References
    512. 

  512. 

  513. </pre>
    514. 

  514. </div>
    515. 

  515.       <div class="tab-pane fade " id="LaTeX" role="tabpanel" aria-labelledby="LaTeX-tab"><pre>Results included in this manuscript come from preprocessing performed
    516. 

  516. using \emph{fMRIPrep} 20.0.6 (\citet{fmriprep1}; \citet{fmriprep2};
    517. 

  517. RRID:SCR\_016216), which is based on \emph{Nipype} 1.4.2
    518. 

  518. (\citet{nipype1}; \citet{nipype2}; RRID:SCR\_002502).
    519. 

  519. 

  520. \begin{description}
    521. 

  521. \item[Anatomical data preprocessing]
    522. 

  522. The T1-weighted (T1w) image was corrected for intensity non-uniformity
    523. 

  523. (INU) with \texttt{N4BiasFieldCorrection} \citep{n4}, distributed with
    524. 

  524. ANTs 2.2.0 \citep[RRID:SCR\_004757]{ants}, and used as T1w-reference
    525. 

  525. throughout the workflow. The T1w-reference was then skull-stripped with
    526. 

  526. a \emph{Nipype} implementation of the \texttt{antsBrainExtraction.sh}
    527. 

  527. workflow (from ANTs), using OASIS30ANTs as target template. Brain tissue
    528. 

  528. segmentation of cerebrospinal fluid (CSF), white-matter (WM) and
    529. 

  529. gray-matter (GM) was performed on the brain-extracted T1w using
    530. 

  530. \texttt{fast} \citep[FSL 5.0.9, RRID:SCR\_002823,][]{fsl_fast}.
    531. 

  531. Volume-based spatial normalization to one standard space
    532. 

  532. (MNI152NLin2009cAsym) was performed through nonlinear registration with
    533. 

  533. \texttt{antsRegistration} (ANTs 2.2.0), using brain-extracted versions
    534. 

  534. of both T1w reference and the T1w template. The following template was
    535. 

  535. selected for spatial normalization: \emph{ICBM 152 Nonlinear
    536. 

  536. Asymmetrical template version 2009c} {[}\citet{mni152nlin2009casym},
    537. 

  537. RRID:SCR\_008796; TemplateFlow ID: MNI152NLin2009cAsym{]},
    538. 

  538. \item[Functional data preprocessing]
    539. 

  539. For each of the 3 BOLD runs found per subject (across all tasks and
    540. 

  540. sessions), the following preprocessing was performed. First, a reference
    541. 

  541. volume and its skull-stripped version were generated using a custom
    542. 

  542. methodology of \emph{fMRIPrep}. Susceptibility distortion correction
    543. 

  543. (SDC) was omitted. The BOLD reference was then co-registered to the T1w
    544. 

  544. reference using \texttt{flirt} \citep[FSL 5.0.9,][]{flirt} with the
    545. 

  545. boundary-based registration \citep{bbr} cost-function. Co-registration
    546. 

  546. was configured with nine degrees of freedom to account for distortions
    547. 

  547. remaining in the BOLD reference. Head-motion parameters with respect to
    548. 

  548. the BOLD reference (transformation matrices, and six corresponding
    549. 

  549. rotation and translation parameters) are estimated before any
    550. 

  550. spatiotemporal filtering using \texttt{mcflirt} \citep[FSL
    551. 

  551. 5.0.9,][]{mcflirt}. The BOLD time-series (including slice-timing
    552. 

  552. correction when applied) were resampled onto their original, native
    553. 

  553. space by applying the transforms to correct for head-motion. These
    554. 

  554. resampled BOLD time-series will be referred to as \emph{preprocessed
    555. 

  555. BOLD in original space}, or just \emph{preprocessed BOLD}. The BOLD
    556. 

  556. time-series were resampled into standard space, generating a
    557. 

  557. \emph{preprocessed BOLD run in MNI152NLin2009cAsym space}. First, a
    558. 

  558. reference volume and its skull-stripped version were generated using a
    559. 

  559. custom methodology of \emph{fMRIPrep}. Several confounding time-series
    560. 

  560. were calculated based on the \emph{preprocessed BOLD}: framewise
    561. 

  561. displacement (FD), DVARS and three region-wise global signals. FD and
    562. 

  562. DVARS are calculated for each functional run, both using their
    563. 

  563. implementations in \emph{Nipype} \citep[following the definitions
    564. 

  564. by][]{power_fd_dvars}. The three global signals are extracted within the
    565. 

  565. CSF, the WM, and the whole-brain masks. Additionally, a set of
    566. 

  566. physiological regressors were extracted to allow for component-based
    567. 

  567. noise correction \citep[\emph{CompCor},][]{compcor}. Principal
    568. 

  568. components are estimated after high-pass filtering the
    569. 

  569. \emph{preprocessed BOLD} time-series (using a discrete cosine filter
    570. 

  570. with 128s cut-off) for the two \emph{CompCor} variants: temporal
    571. 

  571. (tCompCor) and anatomical (aCompCor). tCompCor components are then
    572. 

  572. calculated from the top 5\% variable voxels within a mask covering the
    573. 

  573. subcortical regions. This subcortical mask is obtained by heavily
    574. 

  574. eroding the brain mask, which ensures it does not include cortical GM
    575. 

  575. regions. For aCompCor, components are calculated within the intersection
    576. 

  576. of the aforementioned mask and the union of CSF and WM masks calculated
    577. 

  577. in T1w space, after their projection to the native space of each
    578. 

  578. functional run (using the inverse BOLD-to-T1w transformation).
    579. 

  579. Components are also calculated separately within the WM and CSF masks.
    580. 

  580. For each CompCor decomposition, the \emph{k} components with the largest
    581. 

  581. singular values are retained, such that the retained components' time
    582. 

  582. series are sufficient to explain 50 percent of variance across the
    583. 

  583. nuisance mask (CSF, WM, combined, or temporal). The remaining components
    584. 

  584. are dropped from consideration. The head-motion estimates calculated in
    585. 

  585. the correction step were also placed within the corresponding confounds
    586. 

  586. file. The confound time series derived from head motion estimates and
    587. 

  587. global signals were expanded with the inclusion of temporal derivatives
    588. 

  588. and quadratic terms for each \citep{confounds_satterthwaite_2013}.
    589. 

  589. Frames that exceeded a threshold of 0.5 mm FD or 1.5 standardised DVARS
    590. 

  590. were annotated as motion outliers. All resamplings can be performed with
    591. 

  591. \emph{a single interpolation step} by composing all the pertinent
    592. 

  592. transformations (i.e.~head-motion transform matrices, susceptibility
    593. 

  593. distortion correction when available, and co-registrations to anatomical
    594. 

  594. and output spaces). Gridded (volumetric) resamplings were performed
    595. 

  595. using \texttt{antsApplyTransforms} (ANTs), configured with Lanczos
    596. 

  596. interpolation to minimize the smoothing effects of other kernels
    597. 

  597. \citep{lanczos}. Non-gridded (surface) resamplings were performed using
    598. 

  598. \texttt{mri\_vol2surf} (FreeSurfer).
    599. 

  599. \end{description}
    600. 

  600. 

  601. Many internal operations of \emph{fMRIPrep} use \emph{Nilearn} 0.6.2
    602. 

  602. \citep[RRID:SCR\_001362]{nilearn}, mostly within the functional
    603. 

  603. processing workflow. For more details of the pipeline, see
    604. 

  604. \href{https://fmriprep.readthedocs.io/en/latest/workflows.html}{the
    605. 

  605. section corresponding to workflows in \emph{fMRIPrep}'s documentation}.
    606. 

  606. 

  607. \hypertarget{copyright-waiver}{%
    608. 

  608. \subsubsection{Copyright Waiver}\label{copyright-waiver}}
    609. 

  609. 

  610. The above boilerplate text was automatically generated by fMRIPrep with
    611. 

  611. the express intention that users should copy and paste this text into
    612. 

  612. their manuscripts \emph{unchanged}. It is released under the
    613. 

  613. \href{https://creativecommons.org/publicdomain/zero/1.0/}{CC0} license.
    614. 

  614. 

  615. \hypertarget{references}{%
    616. 

  616. \subsubsection{References}\label{references}}
    617. 

  617. 

  618. \bibliography{/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/data/boilerplate.bib}</pre>
    619. 

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  961. </div>
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  962.     </div>
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  963. </div>
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  964. 

  965. <div id="errors">
    966. 

  966.     <h1 class="sub-report-title">Errors</h1>
    967. 

  967.     <p>No errors to report!</p>
    968. 

  968. </div>
    969. 

  969. 

  970. 

  971. <script type="text/javascript">
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