sub-34.html 116 KB

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  44. <nav class="navbar fixed-top navbar-expand-lg navbar-light bg-light">
  45. <div class="collapse navbar-collapse">
  46. <ul class="navbar-nav">
  47. <li class="nav-item"><a class="nav-link" href="#Summary">Summary</a></li>
  48. <li class="nav-item"><a class="nav-link" href="#Anatomical">Anatomical</a></li>
  49. <li class="nav-item dropdown">
  50. <a class="nav-link dropdown-toggle" id="navbarFunctional" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false" href="#">Functional</a>
  51. <div class="dropdown-menu" aria-labelledby="navbarFunctional">
  52. <a class="dropdown-item" href="#ses-01_task-highspeed_rec-prenorm_run-01"> Session: 01 Task: highspeed Reconstruction: prenorm Run: 01</a>
  53. <a class="dropdown-item" href="#ses-01_task-highspeed_rec-prenorm_run-02"> Session: 01 Task: highspeed Reconstruction: prenorm Run: 02</a>
  54. <a class="dropdown-item" href="#ses-01_task-highspeed_rec-prenorm_run-03"> Session: 01 Task: highspeed Reconstruction: prenorm Run: 03</a>
  55. <a class="dropdown-item" href="#ses-01_task-highspeed_rec-prenorm_run-04"> Session: 01 Task: highspeed Reconstruction: prenorm Run: 04</a>
  56. <a class="dropdown-item" href="#ses-01_task-rest_rec-prenorm_run-post"> Session: 01 Task: rest Reconstruction: prenorm Run: post</a>
  57. <a class="dropdown-item" href="#ses-01_task-rest_rec-prenorm_run-pre"> Session: 01 Task: rest Reconstruction: prenorm Run: pre</a>
  58. <a class="dropdown-item" href="#ses-02_task-highspeed_rec-prenorm_run-01"> Session: 02 Task: highspeed Reconstruction: prenorm Run: 01</a>
  59. <a class="dropdown-item" href="#ses-02_task-highspeed_rec-prenorm_run-02"> Session: 02 Task: highspeed Reconstruction: prenorm Run: 02</a>
  60. <a class="dropdown-item" href="#ses-02_task-highspeed_rec-prenorm_run-03"> Session: 02 Task: highspeed Reconstruction: prenorm Run: 03</a>
  61. <a class="dropdown-item" href="#ses-02_task-highspeed_rec-prenorm_run-04"> Session: 02 Task: highspeed Reconstruction: prenorm Run: 04</a>
  62. <a class="dropdown-item" href="#ses-02_task-rest_rec-prenorm_run-post"> Session: 02 Task: rest Reconstruction: prenorm Run: post</a>
  63. <a class="dropdown-item" href="#ses-02_task-rest_rec-prenorm_run-pre"> Session: 02 Task: rest Reconstruction: prenorm Run: pre</a>
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  65. </li>
  66. <li class="nav-item"><a class="nav-link" href="#About">About</a></li>
  67. <li class="nav-item"><a class="nav-link" href="#boilerplate">Methods</a></li>
  68. <li class="nav-item"><a class="nav-link" href="#errors">Errors</a></li>
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  72. <noscript>
  73. <h1 class="text-danger"> The navigation menu uses Javascript. Without it this report might not work as expected </h1>
  74. </noscript>
  75. <div id="Summary">
  76. <h1 class="sub-report-title">Summary</h1>
  77. <ul class="elem-desc">
  78. <li>Subject ID: sub-34</li>
  79. <li>Structural images: 2 T1-weighted </li>
  80. <li>Functional series: 12</li>
  81. <ul class="elem-desc">
  82. <li>Task: highspeed (8 runs)</li>
  83. <li>Task: rest (4 runs)</li>
  84. </ul>
  85. <li>Resampling targets: T1w, fsnative, MNI152NLin2009cAsym, fsaverage
  86. <li>FreeSurfer reconstruction: Run by fMRIPrep</li>
  87. </ul> </div>
  88. <div id="Anatomical">
  89. <h1 class="sub-report-title">Anatomical</h1>
  90. <h3 class="elem-title">Anatomical Conformation</h3>
  91. <ul class="elem-desc">
  92. <li>Input T1w images: 2</li>
  93. <li>Output orientation: RAS</li>
  94. <li>Output dimensions: 192x256x256</li>
  95. <li>Output voxel size: 1mm x 1mm x 1mm</li>
  96. <li>Discarded images: 0</li>
  97. </ul><h3 class="elem-title">Brain mask and brain tissue segmentation of the T1w</h3><p class="elem-desc">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><br /> <div class="elem-image">
  98. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_seg_brainmask.svg">filename:sub-34/figures/sub-34_seg_brainmask.svg</object>
  99. </div>
  100. <div class="elem-filename">
  101. Get figure file: <a href="./sub-34/figures/sub-34_seg_brainmask.svg" target="_blank">sub-34/figures/sub-34_seg_brainmask.svg</a>
  102. </div>
  103. <h3 class="elem-title">T1 to MNI registration</h3><p class="elem-desc">Nonlinear mapping of the T1w image into MNI space. Hover on the panel with the mouse to transition between both spaces.<p><br /> <div class="elem-image">
  104. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_t1_2_mni.svg">filename:sub-34/figures/sub-34_t1_2_mni.svg</object>
  105. </div>
  106. <div class="elem-filename">
  107. Get figure file: <a href="./sub-34/figures/sub-34_t1_2_mni.svg" target="_blank">sub-34/figures/sub-34_t1_2_mni.svg</a>
  108. </div>
  109. <h3 class="elem-title">Surface reconstruction</h3><p class="elem-desc">Surfaces (white and pial) reconstructed with FreeSurfer (<code>recon-all</code>) overlaid on the participant's T1w template.<p><br /> <div class="elem-image">
  110. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_reconall.svg">filename:sub-34/figures/sub-34_reconall.svg</object>
  111. </div>
  112. <div class="elem-filename">
  113. Get figure file: <a href="./sub-34/figures/sub-34_reconall.svg" target="_blank">sub-34/figures/sub-34_reconall.svg</a>
  114. </div>
  115. </div>
  116. <div id="Functional">
  117. <h1 class="sub-report-title">Functional</h1>
  118. <div id="ses-01_task-highspeed_rec-prenorm_run-01">
  119. <h2 class="run-title">Reports for Session: 01 Task: highspeed Reconstruction: prenorm Run: 01</h2>
  120. <h3 class="elem-title">Summary</h3>
  121. <ul class="elem-desc">
  122. <li>Phase-encoding (PE) direction: Anterior-Posterior</li>
  123. <li>Slice timing correction: Applied</li>
  124. <li>Susceptibility distortion correction: PEB/PEPOLAR (phase-encoding based / PE-POLARity)</li>
  125. <li>Registration: FreeSurfer <code>bbregister</code> (boundary-based registration, BBR) - 6 dof</li>
  126. <li>Functional series resampled to spaces: T1w, fsnative, template, fsaverage</li>
  127. <li>Confounds collected: csf, white_matter, global_signal, 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, a_comp_cor_00, a_comp_cor_01, a_comp_cor_02, a_comp_cor_03, a_comp_cor_04, a_comp_cor_05, cosine00, cosine01, cosine02, cosine03, cosine04, cosine05, cosine06, cosine07, cosine08, non_steady_state_outlier00, non_steady_state_outlier01, non_steady_state_outlier02, trans_x, trans_y, trans_z, rot_x, rot_y, rot_z</li>
  128. </ul><h3 class="elem-title">Note on orientation: qform matrix overwritten</h3>
  129. <p class="elem-desc">The qform has been copied from sform.</p><h3 class="elem-title">Susceptibility distortion correction</h3><p class="elem-desc">Results of performing susceptibility distortion correction (SDC) on the EPI<p> <div class="elem-image">
  130. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-01_sdc_epi.svg">
  131. Problem loading figure sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-01_sdc_epi.svg. If the link below works, please try reloading the report in your browser.</object>
  132. </div>
  133. <div class="elem-filename">
  134. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-01_sdc_epi.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-01_sdc_epi.svg</a>
  135. </div>
  136. <h3 class="elem-title">ROIs in BOLD space</h3><p class="elem-desc">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> <div class="elem-image">
  137. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-01_rois.svg">
  138. Problem loading figure sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-01_rois.svg. If the link below works, please try reloading the report in your browser.</object>
  139. </div>
  140. <div class="elem-filename">
  141. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-01_rois.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-01_rois.svg</a>
  142. </div>
  143. <h3 class="elem-title">EPI to T1 registration</h3><p class="elem-desc"><code>bbregister</code> was used to generate transformations from EPI-space to T1w-space<p> <div class="elem-image">
  144. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-01_bbregister.svg">
  145. Problem loading figure sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-01_bbregister.svg. If the link below works, please try reloading the report in your browser.</object>
  146. </div>
  147. <div class="elem-filename">
  148. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-01_bbregister.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-01_bbregister.svg</a>
  149. </div>
  150. <h3 class="elem-title">BOLD Summary</h3><p class="elem-desc">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> <div class="elem-image">
  151. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-01_carpetplot.svg">
  152. Problem loading figure sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-01_carpetplot.svg. If the link below works, please try reloading the report in your browser.</object>
  153. </div>
  154. <div class="elem-filename">
  155. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-01_carpetplot.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-01_carpetplot.svg</a>
  156. </div>
  157. </div>
  158. <div id="ses-01_task-highspeed_rec-prenorm_run-02">
  159. <h2 class="run-title">Reports for Session: 01 Task: highspeed Reconstruction: prenorm Run: 02</h2>
  160. <h3 class="elem-title">Summary</h3>
  161. <ul class="elem-desc">
  162. <li>Phase-encoding (PE) direction: Anterior-Posterior</li>
  163. <li>Slice timing correction: Applied</li>
  164. <li>Susceptibility distortion correction: PEB/PEPOLAR (phase-encoding based / PE-POLARity)</li>
  165. <li>Registration: FreeSurfer <code>bbregister</code> (boundary-based registration, BBR) - 6 dof</li>
  166. <li>Functional series resampled to spaces: T1w, fsnative, template, fsaverage</li>
  167. <li>Confounds collected: csf, white_matter, global_signal, 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, a_comp_cor_00, a_comp_cor_01, a_comp_cor_02, a_comp_cor_03, a_comp_cor_04, a_comp_cor_05, cosine00, cosine01, cosine02, cosine03, cosine04, cosine05, cosine06, cosine07, cosine08, trans_x, trans_y, trans_z, rot_x, rot_y, rot_z</li>
  168. </ul><h3 class="elem-title">Note on orientation: qform matrix overwritten</h3>
  169. <p class="elem-desc">The qform has been copied from sform.</p><h3 class="elem-title">Susceptibility distortion correction</h3><p class="elem-desc">Results of performing susceptibility distortion correction (SDC) on the EPI<p> <div class="elem-image">
  170. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-02_sdc_epi.svg">
  171. Problem loading figure sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-02_sdc_epi.svg. If the link below works, please try reloading the report in your browser.</object>
  172. </div>
  173. <div class="elem-filename">
  174. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-02_sdc_epi.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-02_sdc_epi.svg</a>
  175. </div>
  176. <h3 class="elem-title">ROIs in BOLD space</h3><p class="elem-desc">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> <div class="elem-image">
  177. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-02_rois.svg">
  178. Problem loading figure sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-02_rois.svg. If the link below works, please try reloading the report in your browser.</object>
  179. </div>
  180. <div class="elem-filename">
  181. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-02_rois.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-02_rois.svg</a>
  182. </div>
  183. <h3 class="elem-title">EPI to T1 registration</h3><p class="elem-desc"><code>bbregister</code> was used to generate transformations from EPI-space to T1w-space<p> <div class="elem-image">
  184. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-02_bbregister.svg">
  185. Problem loading figure sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-02_bbregister.svg. If the link below works, please try reloading the report in your browser.</object>
  186. </div>
  187. <div class="elem-filename">
  188. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-02_bbregister.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-02_bbregister.svg</a>
  189. </div>
  190. <h3 class="elem-title">BOLD Summary</h3><p class="elem-desc">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> <div class="elem-image">
  191. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-02_carpetplot.svg">
  192. Problem loading figure sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-02_carpetplot.svg. If the link below works, please try reloading the report in your browser.</object>
  193. </div>
  194. <div class="elem-filename">
  195. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-02_carpetplot.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-02_carpetplot.svg</a>
  196. </div>
  197. </div>
  198. <div id="ses-01_task-highspeed_rec-prenorm_run-03">
  199. <h2 class="run-title">Reports for Session: 01 Task: highspeed Reconstruction: prenorm Run: 03</h2>
  200. <h3 class="elem-title">Summary</h3>
  201. <ul class="elem-desc">
  202. <li>Phase-encoding (PE) direction: Anterior-Posterior</li>
  203. <li>Slice timing correction: Applied</li>
  204. <li>Susceptibility distortion correction: PEB/PEPOLAR (phase-encoding based / PE-POLARity)</li>
  205. <li>Registration: FreeSurfer <code>bbregister</code> (boundary-based registration, BBR) - 6 dof</li>
  206. <li>Functional series resampled to spaces: T1w, fsnative, template, fsaverage</li>
  207. <li>Confounds collected: csf, white_matter, global_signal, 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, a_comp_cor_00, a_comp_cor_01, a_comp_cor_02, a_comp_cor_03, a_comp_cor_04, a_comp_cor_05, cosine00, cosine01, cosine02, cosine03, cosine04, cosine05, cosine06, cosine07, cosine08, trans_x, trans_y, trans_z, rot_x, rot_y, rot_z</li>
  208. </ul><h3 class="elem-title">Note on orientation: qform matrix overwritten</h3>
  209. <p class="elem-desc">The qform has been copied from sform.</p><h3 class="elem-title">Susceptibility distortion correction</h3><p class="elem-desc">Results of performing susceptibility distortion correction (SDC) on the EPI<p> <div class="elem-image">
  210. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-03_sdc_epi.svg">
  211. Problem loading figure sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-03_sdc_epi.svg. If the link below works, please try reloading the report in your browser.</object>
  212. </div>
  213. <div class="elem-filename">
  214. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-03_sdc_epi.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-03_sdc_epi.svg</a>
  215. </div>
  216. <h3 class="elem-title">ROIs in BOLD space</h3><p class="elem-desc">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> <div class="elem-image">
  217. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-03_rois.svg">
  218. Problem loading figure sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-03_rois.svg. If the link below works, please try reloading the report in your browser.</object>
  219. </div>
  220. <div class="elem-filename">
  221. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-03_rois.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-03_rois.svg</a>
  222. </div>
  223. <h3 class="elem-title">EPI to T1 registration</h3><p class="elem-desc"><code>bbregister</code> was used to generate transformations from EPI-space to T1w-space<p> <div class="elem-image">
  224. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-03_bbregister.svg">
  225. Problem loading figure sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-03_bbregister.svg. If the link below works, please try reloading the report in your browser.</object>
  226. </div>
  227. <div class="elem-filename">
  228. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-03_bbregister.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-03_bbregister.svg</a>
  229. </div>
  230. <h3 class="elem-title">BOLD Summary</h3><p class="elem-desc">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> <div class="elem-image">
  231. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-03_carpetplot.svg">
  232. Problem loading figure sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-03_carpetplot.svg. If the link below works, please try reloading the report in your browser.</object>
  233. </div>
  234. <div class="elem-filename">
  235. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-03_carpetplot.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-03_carpetplot.svg</a>
  236. </div>
  237. </div>
  238. <div id="ses-01_task-highspeed_rec-prenorm_run-04">
  239. <h2 class="run-title">Reports for Session: 01 Task: highspeed Reconstruction: prenorm Run: 04</h2>
  240. <h3 class="elem-title">Summary</h3>
  241. <ul class="elem-desc">
  242. <li>Phase-encoding (PE) direction: Anterior-Posterior</li>
  243. <li>Slice timing correction: Applied</li>
  244. <li>Susceptibility distortion correction: PEB/PEPOLAR (phase-encoding based / PE-POLARity)</li>
  245. <li>Registration: FreeSurfer <code>bbregister</code> (boundary-based registration, BBR) - 6 dof</li>
  246. <li>Functional series resampled to spaces: T1w, fsnative, template, fsaverage</li>
  247. <li>Confounds collected: csf, white_matter, global_signal, 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, a_comp_cor_00, a_comp_cor_01, a_comp_cor_02, a_comp_cor_03, a_comp_cor_04, a_comp_cor_05, cosine00, cosine01, cosine02, cosine03, cosine04, cosine05, cosine06, cosine07, cosine08, trans_x, trans_y, trans_z, rot_x, rot_y, rot_z</li>
  248. </ul><h3 class="elem-title">Note on orientation: qform matrix overwritten</h3>
  249. <p class="elem-desc">The qform has been copied from sform.</p><h3 class="elem-title">Susceptibility distortion correction</h3><p class="elem-desc">Results of performing susceptibility distortion correction (SDC) on the EPI<p> <div class="elem-image">
  250. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-04_sdc_epi.svg">
  251. Problem loading figure sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-04_sdc_epi.svg. If the link below works, please try reloading the report in your browser.</object>
  252. </div>
  253. <div class="elem-filename">
  254. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-04_sdc_epi.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-04_sdc_epi.svg</a>
  255. </div>
  256. <h3 class="elem-title">ROIs in BOLD space</h3><p class="elem-desc">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> <div class="elem-image">
  257. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-04_rois.svg">
  258. Problem loading figure sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-04_rois.svg. If the link below works, please try reloading the report in your browser.</object>
  259. </div>
  260. <div class="elem-filename">
  261. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-04_rois.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-04_rois.svg</a>
  262. </div>
  263. <h3 class="elem-title">EPI to T1 registration</h3><p class="elem-desc"><code>bbregister</code> was used to generate transformations from EPI-space to T1w-space<p> <div class="elem-image">
  264. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-04_bbregister.svg">
  265. Problem loading figure sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-04_bbregister.svg. If the link below works, please try reloading the report in your browser.</object>
  266. </div>
  267. <div class="elem-filename">
  268. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-04_bbregister.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-04_bbregister.svg</a>
  269. </div>
  270. <h3 class="elem-title">BOLD Summary</h3><p class="elem-desc">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> <div class="elem-image">
  271. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-04_carpetplot.svg">
  272. Problem loading figure sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-04_carpetplot.svg. If the link below works, please try reloading the report in your browser.</object>
  273. </div>
  274. <div class="elem-filename">
  275. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-04_carpetplot.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-highspeed_rec-prenorm_run-04_carpetplot.svg</a>
  276. </div>
  277. </div>
  278. <div id="ses-01_task-rest_rec-prenorm_run-post">
  279. <h2 class="run-title">Reports for Session: 01 Task: rest Reconstruction: prenorm Run: post</h2>
  280. <h3 class="elem-title">Summary</h3>
  281. <ul class="elem-desc">
  282. <li>Phase-encoding (PE) direction: Anterior-Posterior</li>
  283. <li>Slice timing correction: Applied</li>
  284. <li>Susceptibility distortion correction: PEB/PEPOLAR (phase-encoding based / PE-POLARity)</li>
  285. <li>Registration: FreeSurfer <code>bbregister</code> (boundary-based registration, BBR) - 6 dof</li>
  286. <li>Functional series resampled to spaces: T1w, fsnative, template, fsaverage</li>
  287. <li>Confounds collected: csf, white_matter, global_signal, 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, a_comp_cor_00, a_comp_cor_01, a_comp_cor_02, a_comp_cor_03, a_comp_cor_04, a_comp_cor_05, cosine00, cosine01, cosine02, non_steady_state_outlier00, non_steady_state_outlier01, trans_x, trans_y, trans_z, rot_x, rot_y, rot_z</li>
  288. </ul><h3 class="elem-title">Note on orientation: qform matrix overwritten</h3>
  289. <p class="elem-desc">The qform has been copied from sform.</p><h3 class="elem-title">Susceptibility distortion correction</h3><p class="elem-desc">Results of performing susceptibility distortion correction (SDC) on the EPI<p> <div class="elem-image">
  290. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-post_sdc_epi.svg">
  291. Problem loading figure sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-post_sdc_epi.svg. If the link below works, please try reloading the report in your browser.</object>
  292. </div>
  293. <div class="elem-filename">
  294. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-post_sdc_epi.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-post_sdc_epi.svg</a>
  295. </div>
  296. <h3 class="elem-title">ROIs in BOLD space</h3><p class="elem-desc">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> <div class="elem-image">
  297. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-post_rois.svg">
  298. Problem loading figure sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-post_rois.svg. If the link below works, please try reloading the report in your browser.</object>
  299. </div>
  300. <div class="elem-filename">
  301. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-post_rois.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-post_rois.svg</a>
  302. </div>
  303. <h3 class="elem-title">EPI to T1 registration</h3><p class="elem-desc"><code>bbregister</code> was used to generate transformations from EPI-space to T1w-space<p> <div class="elem-image">
  304. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-post_bbregister.svg">
  305. Problem loading figure sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-post_bbregister.svg. If the link below works, please try reloading the report in your browser.</object>
  306. </div>
  307. <div class="elem-filename">
  308. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-post_bbregister.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-post_bbregister.svg</a>
  309. </div>
  310. <h3 class="elem-title">BOLD Summary</h3><p class="elem-desc">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> <div class="elem-image">
  311. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-post_carpetplot.svg">
  312. Problem loading figure sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-post_carpetplot.svg. If the link below works, please try reloading the report in your browser.</object>
  313. </div>
  314. <div class="elem-filename">
  315. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-post_carpetplot.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-post_carpetplot.svg</a>
  316. </div>
  317. </div>
  318. <div id="ses-01_task-rest_rec-prenorm_run-pre">
  319. <h2 class="run-title">Reports for Session: 01 Task: rest Reconstruction: prenorm Run: pre</h2>
  320. <h3 class="elem-title">Summary</h3>
  321. <ul class="elem-desc">
  322. <li>Phase-encoding (PE) direction: Anterior-Posterior</li>
  323. <li>Slice timing correction: Applied</li>
  324. <li>Susceptibility distortion correction: PEB/PEPOLAR (phase-encoding based / PE-POLARity)</li>
  325. <li>Registration: FreeSurfer <code>bbregister</code> (boundary-based registration, BBR) - 6 dof</li>
  326. <li>Functional series resampled to spaces: T1w, fsnative, template, fsaverage</li>
  327. <li>Confounds collected: csf, white_matter, global_signal, 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, a_comp_cor_00, a_comp_cor_01, a_comp_cor_02, a_comp_cor_03, a_comp_cor_04, a_comp_cor_05, cosine00, cosine01, cosine02, trans_x, trans_y, trans_z, rot_x, rot_y, rot_z</li>
  328. </ul><h3 class="elem-title">Note on orientation: qform matrix overwritten</h3>
  329. <p class="elem-desc">The qform has been copied from sform.</p><h3 class="elem-title">Susceptibility distortion correction</h3><p class="elem-desc">Results of performing susceptibility distortion correction (SDC) on the EPI<p> <div class="elem-image">
  330. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-pre_sdc_epi.svg">
  331. Problem loading figure sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-pre_sdc_epi.svg. If the link below works, please try reloading the report in your browser.</object>
  332. </div>
  333. <div class="elem-filename">
  334. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-pre_sdc_epi.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-pre_sdc_epi.svg</a>
  335. </div>
  336. <h3 class="elem-title">ROIs in BOLD space</h3><p class="elem-desc">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> <div class="elem-image">
  337. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-pre_rois.svg">
  338. Problem loading figure sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-pre_rois.svg. If the link below works, please try reloading the report in your browser.</object>
  339. </div>
  340. <div class="elem-filename">
  341. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-pre_rois.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-pre_rois.svg</a>
  342. </div>
  343. <h3 class="elem-title">EPI to T1 registration</h3><p class="elem-desc"><code>bbregister</code> was used to generate transformations from EPI-space to T1w-space<p> <div class="elem-image">
  344. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-pre_bbregister.svg">
  345. Problem loading figure sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-pre_bbregister.svg. If the link below works, please try reloading the report in your browser.</object>
  346. </div>
  347. <div class="elem-filename">
  348. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-pre_bbregister.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-pre_bbregister.svg</a>
  349. </div>
  350. <h3 class="elem-title">BOLD Summary</h3><p class="elem-desc">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> <div class="elem-image">
  351. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-pre_carpetplot.svg">
  352. Problem loading figure sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-pre_carpetplot.svg. If the link below works, please try reloading the report in your browser.</object>
  353. </div>
  354. <div class="elem-filename">
  355. Get figure file: <a href="./sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-pre_carpetplot.svg" target="_blank">sub-34/figures/sub-34_ses-01_task-rest_rec-prenorm_run-pre_carpetplot.svg</a>
  356. </div>
  357. </div>
  358. <div id="ses-02_task-highspeed_rec-prenorm_run-01">
  359. <h2 class="run-title">Reports for Session: 02 Task: highspeed Reconstruction: prenorm Run: 01</h2>
  360. <h3 class="elem-title">Summary</h3>
  361. <ul class="elem-desc">
  362. <li>Phase-encoding (PE) direction: Anterior-Posterior</li>
  363. <li>Slice timing correction: Applied</li>
  364. <li>Susceptibility distortion correction: PEB/PEPOLAR (phase-encoding based / PE-POLARity)</li>
  365. <li>Registration: FreeSurfer <code>bbregister</code> (boundary-based registration, BBR) - 6 dof</li>
  366. <li>Functional series resampled to spaces: T1w, fsnative, template, fsaverage</li>
  367. <li>Confounds collected: csf, white_matter, global_signal, 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, a_comp_cor_00, a_comp_cor_01, a_comp_cor_02, a_comp_cor_03, a_comp_cor_04, a_comp_cor_05, cosine00, cosine01, cosine02, cosine03, cosine04, cosine05, cosine06, cosine07, cosine08, non_steady_state_outlier00, non_steady_state_outlier01, non_steady_state_outlier02, trans_x, trans_y, trans_z, rot_x, rot_y, rot_z</li>
  368. </ul><h3 class="elem-title">Susceptibility distortion correction</h3><p class="elem-desc">Results of performing susceptibility distortion correction (SDC) on the EPI<p> <div class="elem-image">
  369. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-01_sdc_epi.svg">
  370. Problem loading figure sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-01_sdc_epi.svg. If the link below works, please try reloading the report in your browser.</object>
  371. </div>
  372. <div class="elem-filename">
  373. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-01_sdc_epi.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-01_sdc_epi.svg</a>
  374. </div>
  375. <h3 class="elem-title">ROIs in BOLD space</h3><p class="elem-desc">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> <div class="elem-image">
  376. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-01_rois.svg">
  377. Problem loading figure sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-01_rois.svg. If the link below works, please try reloading the report in your browser.</object>
  378. </div>
  379. <div class="elem-filename">
  380. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-01_rois.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-01_rois.svg</a>
  381. </div>
  382. <h3 class="elem-title">EPI to T1 registration</h3><p class="elem-desc"><code>bbregister</code> was used to generate transformations from EPI-space to T1w-space<p> <div class="elem-image">
  383. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-01_bbregister.svg">
  384. Problem loading figure sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-01_bbregister.svg. If the link below works, please try reloading the report in your browser.</object>
  385. </div>
  386. <div class="elem-filename">
  387. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-01_bbregister.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-01_bbregister.svg</a>
  388. </div>
  389. <h3 class="elem-title">BOLD Summary</h3><p class="elem-desc">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> <div class="elem-image">
  390. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-01_carpetplot.svg">
  391. Problem loading figure sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-01_carpetplot.svg. If the link below works, please try reloading the report in your browser.</object>
  392. </div>
  393. <div class="elem-filename">
  394. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-01_carpetplot.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-01_carpetplot.svg</a>
  395. </div>
  396. </div>
  397. <div id="ses-02_task-highspeed_rec-prenorm_run-02">
  398. <h2 class="run-title">Reports for Session: 02 Task: highspeed Reconstruction: prenorm Run: 02</h2>
  399. <h3 class="elem-title">Summary</h3>
  400. <ul class="elem-desc">
  401. <li>Phase-encoding (PE) direction: Anterior-Posterior</li>
  402. <li>Slice timing correction: Applied</li>
  403. <li>Susceptibility distortion correction: PEB/PEPOLAR (phase-encoding based / PE-POLARity)</li>
  404. <li>Registration: FreeSurfer <code>bbregister</code> (boundary-based registration, BBR) - 6 dof</li>
  405. <li>Functional series resampled to spaces: T1w, fsnative, template, fsaverage</li>
  406. <li>Confounds collected: csf, white_matter, global_signal, 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, a_comp_cor_00, a_comp_cor_01, a_comp_cor_02, a_comp_cor_03, a_comp_cor_04, a_comp_cor_05, cosine00, cosine01, cosine02, cosine03, cosine04, cosine05, cosine06, cosine07, cosine08, trans_x, trans_y, trans_z, rot_x, rot_y, rot_z</li>
  407. </ul><h3 class="elem-title">Susceptibility distortion correction</h3><p class="elem-desc">Results of performing susceptibility distortion correction (SDC) on the EPI<p> <div class="elem-image">
  408. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-02_sdc_epi.svg">
  409. Problem loading figure sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-02_sdc_epi.svg. If the link below works, please try reloading the report in your browser.</object>
  410. </div>
  411. <div class="elem-filename">
  412. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-02_sdc_epi.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-02_sdc_epi.svg</a>
  413. </div>
  414. <h3 class="elem-title">ROIs in BOLD space</h3><p class="elem-desc">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> <div class="elem-image">
  415. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-02_rois.svg">
  416. Problem loading figure sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-02_rois.svg. If the link below works, please try reloading the report in your browser.</object>
  417. </div>
  418. <div class="elem-filename">
  419. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-02_rois.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-02_rois.svg</a>
  420. </div>
  421. <h3 class="elem-title">EPI to T1 registration</h3><p class="elem-desc"><code>bbregister</code> was used to generate transformations from EPI-space to T1w-space<p> <div class="elem-image">
  422. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-02_bbregister.svg">
  423. Problem loading figure sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-02_bbregister.svg. If the link below works, please try reloading the report in your browser.</object>
  424. </div>
  425. <div class="elem-filename">
  426. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-02_bbregister.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-02_bbregister.svg</a>
  427. </div>
  428. <h3 class="elem-title">BOLD Summary</h3><p class="elem-desc">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> <div class="elem-image">
  429. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-02_carpetplot.svg">
  430. Problem loading figure sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-02_carpetplot.svg. If the link below works, please try reloading the report in your browser.</object>
  431. </div>
  432. <div class="elem-filename">
  433. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-02_carpetplot.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-02_carpetplot.svg</a>
  434. </div>
  435. </div>
  436. <div id="ses-02_task-highspeed_rec-prenorm_run-03">
  437. <h2 class="run-title">Reports for Session: 02 Task: highspeed Reconstruction: prenorm Run: 03</h2>
  438. <h3 class="elem-title">Summary</h3>
  439. <ul class="elem-desc">
  440. <li>Phase-encoding (PE) direction: Anterior-Posterior</li>
  441. <li>Slice timing correction: Applied</li>
  442. <li>Susceptibility distortion correction: PEB/PEPOLAR (phase-encoding based / PE-POLARity)</li>
  443. <li>Registration: FreeSurfer <code>bbregister</code> (boundary-based registration, BBR) - 6 dof</li>
  444. <li>Functional series resampled to spaces: T1w, fsnative, template, fsaverage</li>
  445. <li>Confounds collected: csf, white_matter, global_signal, 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, a_comp_cor_00, a_comp_cor_01, a_comp_cor_02, a_comp_cor_03, a_comp_cor_04, a_comp_cor_05, cosine00, cosine01, cosine02, cosine03, cosine04, cosine05, cosine06, cosine07, cosine08, trans_x, trans_y, trans_z, rot_x, rot_y, rot_z</li>
  446. </ul><h3 class="elem-title">Susceptibility distortion correction</h3><p class="elem-desc">Results of performing susceptibility distortion correction (SDC) on the EPI<p> <div class="elem-image">
  447. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-03_sdc_epi.svg">
  448. Problem loading figure sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-03_sdc_epi.svg. If the link below works, please try reloading the report in your browser.</object>
  449. </div>
  450. <div class="elem-filename">
  451. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-03_sdc_epi.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-03_sdc_epi.svg</a>
  452. </div>
  453. <h3 class="elem-title">ROIs in BOLD space</h3><p class="elem-desc">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> <div class="elem-image">
  454. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-03_rois.svg">
  455. Problem loading figure sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-03_rois.svg. If the link below works, please try reloading the report in your browser.</object>
  456. </div>
  457. <div class="elem-filename">
  458. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-03_rois.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-03_rois.svg</a>
  459. </div>
  460. <h3 class="elem-title">EPI to T1 registration</h3><p class="elem-desc"><code>bbregister</code> was used to generate transformations from EPI-space to T1w-space<p> <div class="elem-image">
  461. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-03_bbregister.svg">
  462. Problem loading figure sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-03_bbregister.svg. If the link below works, please try reloading the report in your browser.</object>
  463. </div>
  464. <div class="elem-filename">
  465. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-03_bbregister.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-03_bbregister.svg</a>
  466. </div>
  467. <h3 class="elem-title">BOLD Summary</h3><p class="elem-desc">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> <div class="elem-image">
  468. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-03_carpetplot.svg">
  469. Problem loading figure sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-03_carpetplot.svg. If the link below works, please try reloading the report in your browser.</object>
  470. </div>
  471. <div class="elem-filename">
  472. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-03_carpetplot.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-03_carpetplot.svg</a>
  473. </div>
  474. </div>
  475. <div id="ses-02_task-highspeed_rec-prenorm_run-04">
  476. <h2 class="run-title">Reports for Session: 02 Task: highspeed Reconstruction: prenorm Run: 04</h2>
  477. <h3 class="elem-title">Summary</h3>
  478. <ul class="elem-desc">
  479. <li>Phase-encoding (PE) direction: Anterior-Posterior</li>
  480. <li>Slice timing correction: Applied</li>
  481. <li>Susceptibility distortion correction: PEB/PEPOLAR (phase-encoding based / PE-POLARity)</li>
  482. <li>Registration: FreeSurfer <code>bbregister</code> (boundary-based registration, BBR) - 6 dof</li>
  483. <li>Functional series resampled to spaces: T1w, fsnative, template, fsaverage</li>
  484. <li>Confounds collected: csf, white_matter, global_signal, 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, a_comp_cor_00, a_comp_cor_01, a_comp_cor_02, a_comp_cor_03, a_comp_cor_04, a_comp_cor_05, cosine00, cosine01, cosine02, cosine03, cosine04, cosine05, cosine06, cosine07, cosine08, trans_x, trans_y, trans_z, rot_x, rot_y, rot_z</li>
  485. </ul><h3 class="elem-title">Susceptibility distortion correction</h3><p class="elem-desc">Results of performing susceptibility distortion correction (SDC) on the EPI<p> <div class="elem-image">
  486. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-04_sdc_epi.svg">
  487. Problem loading figure sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-04_sdc_epi.svg. If the link below works, please try reloading the report in your browser.</object>
  488. </div>
  489. <div class="elem-filename">
  490. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-04_sdc_epi.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-04_sdc_epi.svg</a>
  491. </div>
  492. <h3 class="elem-title">ROIs in BOLD space</h3><p class="elem-desc">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> <div class="elem-image">
  493. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-04_rois.svg">
  494. Problem loading figure sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-04_rois.svg. If the link below works, please try reloading the report in your browser.</object>
  495. </div>
  496. <div class="elem-filename">
  497. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-04_rois.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-04_rois.svg</a>
  498. </div>
  499. <h3 class="elem-title">EPI to T1 registration</h3><p class="elem-desc"><code>bbregister</code> was used to generate transformations from EPI-space to T1w-space<p> <div class="elem-image">
  500. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-04_bbregister.svg">
  501. Problem loading figure sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-04_bbregister.svg. If the link below works, please try reloading the report in your browser.</object>
  502. </div>
  503. <div class="elem-filename">
  504. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-04_bbregister.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-04_bbregister.svg</a>
  505. </div>
  506. <h3 class="elem-title">BOLD Summary</h3><p class="elem-desc">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> <div class="elem-image">
  507. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-04_carpetplot.svg">
  508. Problem loading figure sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-04_carpetplot.svg. If the link below works, please try reloading the report in your browser.</object>
  509. </div>
  510. <div class="elem-filename">
  511. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-04_carpetplot.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-highspeed_rec-prenorm_run-04_carpetplot.svg</a>
  512. </div>
  513. </div>
  514. <div id="ses-02_task-rest_rec-prenorm_run-post">
  515. <h2 class="run-title">Reports for Session: 02 Task: rest Reconstruction: prenorm Run: post</h2>
  516. <h3 class="elem-title">Summary</h3>
  517. <ul class="elem-desc">
  518. <li>Phase-encoding (PE) direction: Anterior-Posterior</li>
  519. <li>Slice timing correction: Applied</li>
  520. <li>Susceptibility distortion correction: PEB/PEPOLAR (phase-encoding based / PE-POLARity)</li>
  521. <li>Registration: FreeSurfer <code>bbregister</code> (boundary-based registration, BBR) - 6 dof</li>
  522. <li>Functional series resampled to spaces: T1w, fsnative, template, fsaverage</li>
  523. <li>Confounds collected: csf, white_matter, global_signal, 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, a_comp_cor_00, a_comp_cor_01, a_comp_cor_02, a_comp_cor_03, a_comp_cor_04, a_comp_cor_05, cosine00, cosine01, cosine02, trans_x, trans_y, trans_z, rot_x, rot_y, rot_z</li>
  524. </ul><h3 class="elem-title">Susceptibility distortion correction</h3><p class="elem-desc">Results of performing susceptibility distortion correction (SDC) on the EPI<p> <div class="elem-image">
  525. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-post_sdc_epi.svg">
  526. Problem loading figure sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-post_sdc_epi.svg. If the link below works, please try reloading the report in your browser.</object>
  527. </div>
  528. <div class="elem-filename">
  529. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-post_sdc_epi.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-post_sdc_epi.svg</a>
  530. </div>
  531. <h3 class="elem-title">ROIs in BOLD space</h3><p class="elem-desc">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> <div class="elem-image">
  532. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-post_rois.svg">
  533. Problem loading figure sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-post_rois.svg. If the link below works, please try reloading the report in your browser.</object>
  534. </div>
  535. <div class="elem-filename">
  536. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-post_rois.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-post_rois.svg</a>
  537. </div>
  538. <h3 class="elem-title">EPI to T1 registration</h3><p class="elem-desc"><code>bbregister</code> was used to generate transformations from EPI-space to T1w-space<p> <div class="elem-image">
  539. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-post_bbregister.svg">
  540. Problem loading figure sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-post_bbregister.svg. If the link below works, please try reloading the report in your browser.</object>
  541. </div>
  542. <div class="elem-filename">
  543. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-post_bbregister.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-post_bbregister.svg</a>
  544. </div>
  545. <h3 class="elem-title">BOLD Summary</h3><p class="elem-desc">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> <div class="elem-image">
  546. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-post_carpetplot.svg">
  547. Problem loading figure sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-post_carpetplot.svg. If the link below works, please try reloading the report in your browser.</object>
  548. </div>
  549. <div class="elem-filename">
  550. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-post_carpetplot.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-post_carpetplot.svg</a>
  551. </div>
  552. </div>
  553. <div id="ses-02_task-rest_rec-prenorm_run-pre">
  554. <h2 class="run-title">Reports for Session: 02 Task: rest Reconstruction: prenorm Run: pre</h2>
  555. <h3 class="elem-title">Summary</h3>
  556. <ul class="elem-desc">
  557. <li>Phase-encoding (PE) direction: Anterior-Posterior</li>
  558. <li>Slice timing correction: Applied</li>
  559. <li>Susceptibility distortion correction: PEB/PEPOLAR (phase-encoding based / PE-POLARity)</li>
  560. <li>Registration: FreeSurfer <code>bbregister</code> (boundary-based registration, BBR) - 6 dof</li>
  561. <li>Functional series resampled to spaces: T1w, fsnative, template, fsaverage</li>
  562. <li>Confounds collected: csf, white_matter, global_signal, 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, a_comp_cor_00, a_comp_cor_01, a_comp_cor_02, a_comp_cor_03, a_comp_cor_04, a_comp_cor_05, cosine00, cosine01, cosine02, non_steady_state_outlier00, non_steady_state_outlier01, trans_x, trans_y, trans_z, rot_x, rot_y, rot_z</li>
  563. </ul><h3 class="elem-title">Susceptibility distortion correction</h3><p class="elem-desc">Results of performing susceptibility distortion correction (SDC) on the EPI<p> <div class="elem-image">
  564. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-pre_sdc_epi.svg">
  565. Problem loading figure sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-pre_sdc_epi.svg. If the link below works, please try reloading the report in your browser.</object>
  566. </div>
  567. <div class="elem-filename">
  568. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-pre_sdc_epi.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-pre_sdc_epi.svg</a>
  569. </div>
  570. <h3 class="elem-title">ROIs in BOLD space</h3><p class="elem-desc">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> <div class="elem-image">
  571. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-pre_rois.svg">
  572. Problem loading figure sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-pre_rois.svg. If the link below works, please try reloading the report in your browser.</object>
  573. </div>
  574. <div class="elem-filename">
  575. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-pre_rois.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-pre_rois.svg</a>
  576. </div>
  577. <h3 class="elem-title">EPI to T1 registration</h3><p class="elem-desc"><code>bbregister</code> was used to generate transformations from EPI-space to T1w-space<p> <div class="elem-image">
  578. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-pre_bbregister.svg">
  579. Problem loading figure sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-pre_bbregister.svg. If the link below works, please try reloading the report in your browser.</object>
  580. </div>
  581. <div class="elem-filename">
  582. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-pre_bbregister.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-pre_bbregister.svg</a>
  583. </div>
  584. <h3 class="elem-title">BOLD Summary</h3><p class="elem-desc">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> <div class="elem-image">
  585. <object class="svg-reportlet" type="image/svg+xml" data="./sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-pre_carpetplot.svg">
  586. Problem loading figure sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-pre_carpetplot.svg. If the link below works, please try reloading the report in your browser.</object>
  587. </div>
  588. <div class="elem-filename">
  589. Get figure file: <a href="./sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-pre_carpetplot.svg" target="_blank">sub-34/figures/sub-34_ses-02_task-rest_rec-prenorm_run-pre_carpetplot.svg</a>
  590. </div>
  591. </div>
  592. </div>
  593. <div id="About">
  594. <h1 class="sub-report-title">About</h1>
  595. <ul>
  596. <li>FMRIPrep version: 1.2.2</li>
  597. <li>FMRIPrep command: <code>/usr/local/miniconda/bin/fmriprep --fs-license-file /utilities/fs_600_license.txt /input/ /output/ participant --participant_label 34 -w /work/ --mem_mb 35000 --nthreads 8 --omp-nthreads 8 --write-graph --stop-on-first-crash --output-space T1w fsnative template fsaverage --notrack --verbose --resource-monitor</code></li>
  598. <li>Date preprocessed: 2020-09-20 19:41:34 +0000</li>
  599. </ul>
  600. </div> </div>
  601. <div id="boilerplate">
  602. <h1 class="sub-report-title">Methods</h1>
  603. <p>We kindly ask to report results preprocessed with fMRIPrep using the following
  604. boilerplate</p>
  605. <ul class="nav nav-tabs" id="myTab" role="tablist">
  606. <li class="nav-item">
  607. <a class="nav-link active" id="HTML-tab" data-toggle="tab" href="#HTML" role="tab" aria-controls="HTML" aria-selected="true">HTML</a>
  608. </li>
  609. <li class="nav-item">
  610. <a class="nav-link " id="Markdown-tab" data-toggle="tab" href="#Markdown" role="tab" aria-controls="Markdown" aria-selected="false">Markdown</a>
  611. </li>
  612. <li class="nav-item">
  613. <a class="nav-link " id="LaTeX-tab" data-toggle="tab" href="#LaTeX" role="tab" aria-controls="LaTeX" aria-selected="false">LaTeX</a>
  614. </li>
  615. </ul>
  616. <div class="tab-content" id="myTabContent">
  617. <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>fMRIPprep</em> 1.2.2 (<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> 1.1.5 (<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>
  618. <dl>
  619. <dt>Anatomical data preprocessing</dt>
  620. <dd><p>A total of 2 T1-weighted (T1w) images were found within the input BIDS dataset. All of them were corrected for intensity non-uniformity (INU) using <code>N4BiasFieldCorrection</code> <span class="citation" data-cites="n4">(Tustison et al. 2010, ANTs 2.2.0)</span>. A T1w-reference map was computed after registration of 2 T1w images (after INU-correction) using <code>mri_robust_template</code> <span class="citation" data-cites="fs_template">(FreeSurfer 6.0.1, Reuter, Rosas, and Fischl 2010)</span>. The T1w-reference was then skull-stripped using <code>antsBrainExtraction.sh</code> (ANTs 2.2.0), using OASIS as target template. Brain surfaces were reconstructed using <code>recon-all</code> <span class="citation" data-cites="fs_reconall">(FreeSurfer 6.0.1, RRID:SCR_001847, Dale, Fischl, and Sereno 1999)</span>, and the brain mask estimated previously was refined with a custom variation of the method to reconcile ANTs-derived and FreeSurfer-derived segmentations of the cortical gray-matter of Mindboggle <span class="citation" data-cites="mindboggle">(RRID:SCR_002438, Klein et al. 2017)</span>. Spatial normalization to the ICBM 152 Nonlinear Asymmetrical template version 2009c <span class="citation" data-cites="mni">(Fonov et al. 2009, RRID:SCR_008796)</span> was performed through nonlinear registration with <code>antsRegistration</code> <span class="citation" data-cites="ants">(ANTs 2.2.0, RRID:SCR_004757, Avants et al. 2008)</span>, using brain-extracted versions of both T1w volume and 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>.</p>
  621. </dd>
  622. <dt>Functional data preprocessing</dt>
  623. <dd><p>For each of the 12 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>. A deformation field to correct for susceptibility distortions was estimated based on two echo-planar imaging (EPI) references with opposing phase-encoding directions, using <code>3dQwarp</code> <span class="citation" data-cites="afni">Cox and Hyde (1997)</span> (AFNI 20160207). Based on the estimated susceptibility distortion, an unwarped BOLD reference was calculated for a more accurate co-registration with the anatomical reference. The BOLD reference was then co-registered to the T1w reference using <code>bbregister</code> (FreeSurfer) which implements boundary-based registration <span class="citation" data-cites="bbr">(Greve and Fischl 2009)</span>. 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>. BOLD runs were slice-time corrected using <code>3dTshift</code> from AFNI 20160207 <span class="citation" data-cites="afni">(Cox and Hyde 1997, RRID:SCR_005927)</span>. The BOLD time-series (including slice-timing correction when applied) were resampled onto their original, native space by applying a single, composite transform to correct for head-motion and susceptibility distortions. 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 to MNI152NLin2009cAsym 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). Six 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, six 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). The head-motion estimates calculated in the correction step were also placed within the corresponding confounds file. The BOLD time-series, were resampled to surfaces on the following spaces: <em>fsnative</em>, <em>fsaverage</em>. 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 template 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>
  624. </dd>
  625. </dl>
  626. <p>Many internal operations of <em>fMRIPrep</em> use <em>Nilearn</em> 0.4.2 <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>
  627. <h3 id="references" class="unnumbered">References</h3>
  628. <div id="refs" class="references">
  629. <div id="ref-nilearn">
  630. <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>
  631. </div>
  632. <div id="ref-ants">
  633. <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>
  634. </div>
  635. <div id="ref-compcor">
  636. <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>
  637. </div>
  638. <div id="ref-afni">
  639. <p>Cox, Robert W., and James S. Hyde. 1997. “Software Tools for Analysis and Visualization of fMRI Data.” <em>NMR in Biomedicine</em> 10 (4-5): 171–78. <a href="https://doi.org/10.1002/(SICI)1099-1492(199706/08)10:4/5&lt;171::AID-NBM453&gt;3.0.CO;2-L" class="uri">https://doi.org/10.1002/(SICI)1099-1492(199706/08)10:4/5&lt;171::AID-NBM453&gt;3.0.CO;2-L</a>.</p>
  640. </div>
  641. <div id="ref-fs_reconall">
  642. <p>Dale, Anders M., Bruce Fischl, and Martin I. Sereno. 1999. “Cortical Surface-Based Analysis: I. Segmentation and Surface Reconstruction.” <em>NeuroImage</em> 9 (2): 179–94. <a href="https://doi.org/10.1006/nimg.1998.0395" class="uri">https://doi.org/10.1006/nimg.1998.0395</a>.</p>
  643. </div>
  644. <div id="ref-fmriprep2">
  645. <p>Esteban, Oscar, Ross Blair, Christopher J. Markiewicz, Shoshana L. Berleant, Craig Moodie, Feilong Ma, Ayse Ilkay Isik, et al. 2018. “FMRIPrep 1.2.2.” <em>Software</em>. Zenodo. <a href="https://doi.org/10.5281/zenodo.852659" class="uri">https://doi.org/10.5281/zenodo.852659</a>.</p>
  646. </div>
  647. <div id="ref-fmriprep1">
  648. <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>bioRxiv</em>. <a href="https://doi.org/10.1101/306951" class="uri">https://doi.org/10.1101/306951</a>.</p>
  649. </div>
  650. <div id="ref-mni">
  651. <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>, Organization for human brain mapping 2009 annual meeting, 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>
  652. </div>
  653. <div id="ref-nipype1">
  654. <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>
  655. </div>
  656. <div id="ref-nipype2">
  657. <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>
  658. </div>
  659. <div id="ref-bbr">
  660. <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>
  661. </div>
  662. <div id="ref-mcflirt">
  663. <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>
  664. </div>
  665. <div id="ref-mindboggle">
  666. <p>Klein, Arno, Satrajit S. Ghosh, Forrest S. Bao, Joachim Giard, Yrjö Häme, Eliezer Stavsky, Noah Lee, et al. 2017. “Mindboggling Morphometry of Human Brains.” <em>PLOS Computational Biology</em> 13 (2): e1005350. <a href="https://doi.org/10.1371/journal.pcbi.1005350" class="uri">https://doi.org/10.1371/journal.pcbi.1005350</a>.</p>
  667. </div>
  668. <div id="ref-lanczos">
  669. <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>
  670. </div>
  671. <div id="ref-power_fd_dvars">
  672. <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>
  673. </div>
  674. <div id="ref-fs_template">
  675. <p>Reuter, Martin, Herminia Diana Rosas, and Bruce Fischl. 2010. “Highly Accurate Inverse Consistent Registration: A Robust Approach.” <em>NeuroImage</em> 53 (4): 1181–96. <a href="https://doi.org/10.1016/j.neuroimage.2010.07.020" class="uri">https://doi.org/10.1016/j.neuroimage.2010.07.020</a>.</p>
  676. </div>
  677. <div id="ref-n4">
  678. <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>
  679. </div>
  680. <div id="ref-fsl_fast">
  681. <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>
  682. </div>
  683. </div></div></div>
  684. <div class="tab-pane fade " id="Markdown" role="tabpanel" aria-labelledby="Markdown-tab"><pre>
  685. Results included in this manuscript come from preprocessing
  686. performed using *fMRIPprep* 1.2.2
  687. (@fmriprep1; @fmriprep2; RRID:SCR_016216),
  688. which is based on *Nipype* 1.1.5
  689. (@nipype1; @nipype2; RRID:SCR_002502).
  690. Anatomical data preprocessing
  691. : A total of 2 T1-weighted (T1w) images were found within the input
  692. BIDS dataset.
  693. All of them were corrected for intensity non-uniformity (INU)
  694. using `N4BiasFieldCorrection` [@n4, ANTs 2.2.0].
  695. A T1w-reference map was computed after registration of
  696. 2 T1w images (after INU-correction) using
  697. `mri_robust_template` [FreeSurfer 6.0.1, @fs_template].
  698. The T1w-reference was then skull-stripped using `antsBrainExtraction.sh`
  699. (ANTs 2.2.0), using OASIS as target template.
  700. Brain surfaces were reconstructed using `recon-all` [FreeSurfer 6.0.1,
  701. RRID:SCR_001847, @fs_reconall], and the brain mask estimated
  702. previously was refined with a custom variation of the method to reconcile
  703. ANTs-derived and FreeSurfer-derived segmentations of the cortical
  704. gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].
  705. Spatial normalization to the ICBM 152 Nonlinear Asymmetrical
  706. template version 2009c [@mni, RRID:SCR_008796] was performed
  707. through nonlinear registration with `antsRegistration`
  708. [ANTs 2.2.0, RRID:SCR_004757, @ants], using
  709. brain-extracted versions of both T1w volume and template.
  710. Brain tissue segmentation of cerebrospinal fluid (CSF),
  711. white-matter (WM) and gray-matter (GM) was performed on
  712. the brain-extracted T1w using `fast` [FSL 5.0.9, RRID:SCR_002823,
  713. @fsl_fast].
  714. Functional data preprocessing
  715. : For each of the 12 BOLD runs found per subject (across all
  716. tasks and sessions), the following preprocessing was performed.
  717. First, a reference volume and its skull-stripped version were generated
  718. using a custom methodology of *fMRIPrep*.
  719. A deformation field to correct for susceptibility distortions was estimated
  720. based on two echo-planar imaging (EPI) references with opposing phase-encoding
  721. directions, using `3dQwarp` @afni (AFNI 20160207).
  722. Based on the estimated susceptibility distortion, an
  723. unwarped BOLD reference was calculated for a more accurate
  724. co-registration with the anatomical reference.
  725. The BOLD reference was then co-registered to the T1w reference using
  726. `bbregister` (FreeSurfer) which implements boundary-based registration [@bbr].
  727. Co-registration was configured with nine degrees of freedom to account
  728. for distortions remaining in the BOLD reference.
  729. Head-motion parameters with respect to the BOLD reference
  730. (transformation matrices, and six corresponding rotation and translation
  731. parameters) are estimated before any spatiotemporal filtering using
  732. `mcflirt` [FSL 5.0.9, @mcflirt].
  733. BOLD runs were slice-time corrected using `3dTshift` from
  734. AFNI 20160207 [@afni, RRID:SCR_005927].
  735. The BOLD time-series (including slice-timing correction when applied)
  736. were resampled onto their original, native space by applying
  737. a single, composite transform to correct for head-motion and
  738. susceptibility distortions.
  739. These resampled BOLD time-series will be referred to as *preprocessed
  740. BOLD in original space*, or just *preprocessed BOLD*.
  741. The BOLD time-series were resampled to MNI152NLin2009cAsym standard space,
  742. generating a *preprocessed BOLD run in MNI152NLin2009cAsym space*.
  743. First, a reference volume and its skull-stripped version were generated
  744. using a custom methodology of *fMRIPrep*.
  745. Several confounding time-series were calculated based on the
  746. *preprocessed BOLD*: framewise displacement (FD), DVARS and
  747. three region-wise global signals.
  748. FD and DVARS are calculated for each functional run, both using their
  749. implementations in *Nipype* [following the definitions by @power_fd_dvars].
  750. The three global signals are extracted within the CSF, the WM, and
  751. the whole-brain masks.
  752. Additionally, a set of physiological regressors were extracted to
  753. allow for component-based noise correction [*CompCor*, @compcor].
  754. Principal components are estimated after high-pass filtering the
  755. *preprocessed BOLD* time-series (using a discrete cosine filter with
  756. 128s cut-off) for the two *CompCor* variants: temporal (tCompCor)
  757. and anatomical (aCompCor).
  758. Six tCompCor components are then calculated from the top 5% variable
  759. voxels within a mask covering the subcortical regions.
  760. This subcortical mask is obtained by heavily eroding the brain mask,
  761. which ensures it does not include cortical GM regions.
  762. For aCompCor, six components are calculated within the intersection of
  763. the aforementioned mask and the union of CSF and WM masks calculated
  764. in T1w space, after their projection to the native space of each
  765. functional run (using the inverse BOLD-to-T1w transformation).
  766. The head-motion estimates calculated in the correction step were also
  767. placed within the corresponding confounds file.
  768. The BOLD time-series, were resampled to surfaces on the following
  769. spaces: *fsnative*, *fsaverage*.
  770. All resamplings can be performed with *a single interpolation
  771. step* by composing all the pertinent transformations (i.e. head-motion
  772. transform matrices, susceptibility distortion correction when available,
  773. and co-registrations to anatomical and template spaces).
  774. Gridded (volumetric) resamplings were performed using `antsApplyTransforms` (ANTs),
  775. configured with Lanczos interpolation to minimize the smoothing
  776. effects of other kernels [@lanczos].
  777. Non-gridded (surface) resamplings were performed using `mri_vol2surf`
  778. (FreeSurfer).
  779. Many internal operations of *fMRIPrep* use
  780. *Nilearn* 0.4.2 [@nilearn, RRID:SCR_001362],
  781. mostly within the functional processing workflow.
  782. For more details of the pipeline, see [the section corresponding
  783. to workflows in *fMRIPrep*'s documentation](https://fmriprep.readthedocs.io/en/latest/workflows.html "FMRIPrep's documentation").
  784. ### References
  785. </pre>
  786. </div>
  787. <div class="tab-pane fade " id="LaTeX" role="tabpanel" aria-labelledby="LaTeX-tab"><pre>Results included in this manuscript come from preprocessing performed
  788. using \emph{fMRIPprep} 1.2.2 (\citet{fmriprep1}; \citet{fmriprep2};
  789. RRID:SCR\_016216), which is based on \emph{Nipype} 1.1.5
  790. (\citet{nipype1}; \citet{nipype2}; RRID:SCR\_002502).
  791. \begin{description}
  792. \item[Anatomical data preprocessing]
  793. A total of 2 T1-weighted (T1w) images were found within the input BIDS
  794. dataset. All of them were corrected for intensity non-uniformity (INU)
  795. using \texttt{N4BiasFieldCorrection} \citep[ANTs 2.2.0]{n4}. A
  796. T1w-reference map was computed after registration of 2 T1w images (after
  797. INU-correction) using \texttt{mri\_robust\_template} \citep[FreeSurfer
  798. 6.0.1,][]{fs_template}. The T1w-reference was then skull-stripped using
  799. \texttt{antsBrainExtraction.sh} (ANTs 2.2.0), using OASIS as target
  800. template. Brain surfaces were reconstructed using \texttt{recon-all}
  801. \citep[FreeSurfer 6.0.1, RRID:SCR\_001847,][]{fs_reconall}, and the
  802. brain mask estimated previously was refined with a custom variation of
  803. the method to reconcile ANTs-derived and FreeSurfer-derived
  804. segmentations of the cortical gray-matter of Mindboggle
  805. \citep[RRID:SCR\_002438,][]{mindboggle}. Spatial normalization to the
  806. ICBM 152 Nonlinear Asymmetrical template version 2009c
  807. \citep[RRID:SCR\_008796]{mni} was performed through nonlinear
  808. registration with \texttt{antsRegistration} \citep[ANTs 2.2.0,
  809. RRID:SCR\_004757,][]{ants}, using brain-extracted versions of both T1w
  810. volume and template. Brain tissue segmentation of cerebrospinal fluid
  811. (CSF), white-matter (WM) and gray-matter (GM) was performed on the
  812. brain-extracted T1w using \texttt{fast} \citep[FSL 5.0.9,
  813. RRID:SCR\_002823,][]{fsl_fast}.
  814. \item[Functional data preprocessing]
  815. For each of the 12 BOLD runs found per subject (across all tasks and
  816. sessions), the following preprocessing was performed. First, a reference
  817. volume and its skull-stripped version were generated using a custom
  818. methodology of \emph{fMRIPrep}. A deformation field to correct for
  819. susceptibility distortions was estimated based on two echo-planar
  820. imaging (EPI) references with opposing phase-encoding directions, using
  821. \texttt{3dQwarp} \citet{afni} (AFNI 20160207). Based on the estimated
  822. susceptibility distortion, an unwarped BOLD reference was calculated for
  823. a more accurate co-registration with the anatomical reference. The BOLD
  824. reference was then co-registered to the T1w reference using
  825. \texttt{bbregister} (FreeSurfer) which implements boundary-based
  826. registration \citep{bbr}. Co-registration was configured with nine
  827. degrees of freedom to account for distortions remaining in the BOLD
  828. reference. Head-motion parameters with respect to the BOLD reference
  829. (transformation matrices, and six corresponding rotation and translation
  830. parameters) are estimated before any spatiotemporal filtering using
  831. \texttt{mcflirt} \citep[FSL 5.0.9,][]{mcflirt}. BOLD runs were
  832. slice-time corrected using \texttt{3dTshift} from AFNI 20160207
  833. \citep[RRID:SCR\_005927]{afni}. The BOLD time-series (including
  834. slice-timing correction when applied) were resampled onto their
  835. original, native space by applying a single, composite transform to
  836. correct for head-motion and susceptibility distortions. These resampled
  837. BOLD time-series will be referred to as \emph{preprocessed BOLD in
  838. original space}, or just \emph{preprocessed BOLD}. The BOLD time-series
  839. were resampled to MNI152NLin2009cAsym standard space, generating a
  840. \emph{preprocessed BOLD run in MNI152NLin2009cAsym space}. First, a
  841. reference volume and its skull-stripped version were generated using a
  842. custom methodology of \emph{fMRIPrep}. Several confounding time-series
  843. were calculated based on the \emph{preprocessed BOLD}: framewise
  844. displacement (FD), DVARS and three region-wise global signals. FD and
  845. DVARS are calculated for each functional run, both using their
  846. implementations in \emph{Nipype} \citep[following the definitions
  847. by][]{power_fd_dvars}. The three global signals are extracted within the
  848. CSF, the WM, and the whole-brain masks. Additionally, a set of
  849. physiological regressors were extracted to allow for component-based
  850. noise correction \citep[\emph{CompCor},][]{compcor}. Principal
  851. components are estimated after high-pass filtering the
  852. \emph{preprocessed BOLD} time-series (using a discrete cosine filter
  853. with 128s cut-off) for the two \emph{CompCor} variants: temporal
  854. (tCompCor) and anatomical (aCompCor). Six tCompCor components are then
  855. calculated from the top 5\% variable voxels within a mask covering the
  856. subcortical regions. This subcortical mask is obtained by heavily
  857. eroding the brain mask, which ensures it does not include cortical GM
  858. regions. For aCompCor, six components are calculated within the
  859. intersection of the aforementioned mask and the union of CSF and WM
  860. masks calculated in T1w space, after their projection to the native
  861. space of each functional run (using the inverse BOLD-to-T1w
  862. transformation). The head-motion estimates calculated in the correction
  863. step were also placed within the corresponding confounds file. The BOLD
  864. time-series, were resampled to surfaces on the following spaces:
  865. \emph{fsnative}, \emph{fsaverage}. All resamplings can be performed with
  866. \emph{a single interpolation step} by composing all the pertinent
  867. transformations (i.e.~head-motion transform matrices, susceptibility
  868. distortion correction when available, and co-registrations to anatomical
  869. and template spaces). Gridded (volumetric) resamplings were performed
  870. using \texttt{antsApplyTransforms} (ANTs), configured with Lanczos
  871. interpolation to minimize the smoothing effects of other kernels
  872. \citep{lanczos}. Non-gridded (surface) resamplings were performed using
  873. \texttt{mri\_vol2surf} (FreeSurfer).
  874. \end{description}
  875. Many internal operations of \emph{fMRIPrep} use \emph{Nilearn} 0.4.2
  876. \citep[RRID:SCR\_001362]{nilearn}, mostly within the functional
  877. processing workflow. For more details of the pipeline, see
  878. \href{https://fmriprep.readthedocs.io/en/latest/workflows.html}{the
  879. section corresponding to workflows in \emph{fMRIPrep}'s documentation}.
  880. \hypertarget{references}{%
  881. \subsubsection{References}\label{references}}
  882. \bibliography{/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/data/boilerplate.bib}</pre>
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  1162. </pre>
  1163. </div>
  1164. </div>
  1165. <p>Alternatively, an interactive <a href="http://fmriprep.readthedocs.io/en/latest/citing.html">boilerplate generator</a> is available in the <a href="https://fmriprep.org">documentation website</a>.</p>
  1166. </div>
  1167. <div id="errors">
  1168. <h1 class="sub-report-title">Errors</h1>
  1169. <ul>
  1170. <li>No errors to report!</li>
  1171. </ul>
  1172. </div>
  1173. <script type="text/javascript">
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