{"id":671,"date":"2022-11-08T20:47:55","date_gmt":"2022-11-08T20:47:55","guid":{"rendered":"https:\/\/web4.bilkent.edu.tr\/hcf\/?page_id=671"},"modified":"2022-11-08T20:47:55","modified_gmt":"2022-11-08T20:47:55","slug":"pre-processing-quiz","status":"publish","type":"page","link":"https:\/\/web4.bilkent.edu.tr\/hcf\/?page_id=671","title":{"rendered":"Pre-processing quiz"},"content":{"rendered":"\n<h3 class=\"wp-block-heading\">Realignment<\/h3>\n\n\n\n<ul class=\"has-small-font-size\">\n<li>Why do we do realignment?<\/li>\n\n\n\n<li>What is the acceptable movement units? What to do if it&#8217;s higher than the threshold?<\/li>\n\n\n\n<li>How can you check movement of a particular participant?<\/li>\n\n\n\n<li>How can we make our realignment better? What parameter should we modify?<\/li>\n\n\n\n<li>What is the output of realignment? How do we use it in GLM?<\/li>\n\n\n\n<li>When should you realign to the the first, mean or last image when doing realignment?<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Slicetiming correction<\/h3>\n\n\n\n<ul class=\"has-small-font-size\">\n<li>Why do we do slicetiming correction?<\/li>\n\n\n\n<li>What does TR mean?<\/li>\n\n\n\n<li>Why do you think slicetiming correction is important particularly for event related designs?<\/li>\n\n\n\n<li>What parameters do we use while doing slice time correction? Check our EPI sequence and in what way we acquire our slices. <\/li>\n\n\n\n<li>What happens in an interleaved slice acquisition? How does it compare to a descending\/ascending slice acquisition?<\/li>\n\n\n\n<li>Check what caveats there are out there for interleaved slice acquisitions (spin-history effects)<\/li>\n\n\n\n<li>How long does it take for each slice to be acquired?<\/li>\n\n\n\n<li>What do you think the reference slice parameter pertains to? Which reference slice would be better to use? Why\/why not?<\/li>\n\n\n\n<li>What is the output of slicetiming correction?<\/li>\n\n\n\n<li>In our regular EPI protocol, how many slices do we take per TR?<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Normalization<\/h3>\n\n\n\n<ul class=\"has-small-font-size\">\n<li>Why do we normalize?<\/li>\n\n\n\n<li>What is the MNI template? Why is it called MNI152? How was MNI152 &#8220;generated&#8221;?<\/li>\n\n\n\n<li>In what situation do you think we may not want to normalize our images?<\/li>\n\n\n\n<li>What is the output of our normalization?<\/li>\n\n\n\n<li>The normalization parameters which we generate from normalization can be used to do subject space analysis and ROI estimation. What kind of parameters can we be using to do this?<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Smoothing<\/h3>\n\n\n\n<ul class=\"has-small-font-size\">\n<li>Why do we smoothen our data?<\/li>\n\n\n\n<li>When should we not smoothen our data?<\/li>\n\n\n\n<li>How do we smoothen our data? What does the kernel size FWHM correspond to? On what ground do we choose it&#8217;s values?<\/li>\n\n\n\n<li>What is the output of smoothened data?<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Coregisteration \/ Segmentation<\/h3>\n\n\n\n<ul class=\"has-small-font-size\">\n<li>Why do we do and what do we do in coregisteration?<\/li>\n\n\n\n<li>Why do we do and why do we do tissue segmentation?<\/li>\n\n\n\n<li>How do you check if your data is coregistered properly?<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Bias correction<\/h3>\n\n\n\n<ul class=\"has-small-font-size\">\n<li>Why do we do bias correction?<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Realignment Slicetiming correction Normalization Smoothing Coregisteration \/ Segmentation Bias correction<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"om_disable_all_campaigns":false,"_mi_skip_tracking":false},"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/web4.bilkent.edu.tr\/hcf\/index.php?rest_route=\/wp\/v2\/pages\/671"}],"collection":[{"href":"https:\/\/web4.bilkent.edu.tr\/hcf\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/web4.bilkent.edu.tr\/hcf\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/web4.bilkent.edu.tr\/hcf\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/web4.bilkent.edu.tr\/hcf\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=671"}],"version-history":[{"count":25,"href":"https:\/\/web4.bilkent.edu.tr\/hcf\/index.php?rest_route=\/wp\/v2\/pages\/671\/revisions"}],"predecessor-version":[{"id":866,"href":"https:\/\/web4.bilkent.edu.tr\/hcf\/index.php?rest_route=\/wp\/v2\/pages\/671\/revisions\/866"}],"wp:attachment":[{"href":"https:\/\/web4.bilkent.edu.tr\/hcf\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=671"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}