<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On Nov 5, 2014, at 4:49 AM, Mike Strauss wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div><font class="Apple-style-span" color="#1306b1">once you fix the alignment in Midas, and save the transformations, you just need to rerun “Generate Course Aligned Stack” ( think that’s what it’s called). Do NOT run the automatic correlation step again, as that will overwrite your Midas work.</font></div><div><font class="Apple-style-span" color="#1306b1"><br></font></div><div><font class="Apple-style-span" color="#1306b1">As I understand it, the process is as follows:</font></div><div><font class="Apple-style-span" color="#1306b1">-find frame-to-frame transformations (either by correlation or by Midas) - these are saved as a .xf file</font></div><div><font class="Apple-style-span" color="#1306b1">-calculate the global transformations (to retain the majority of the image in the frame) - using xftoxg</font></div><div><font class="Apple-style-span" color="#1306b1">-apply global transformations to the unaligned stack</font></div><div><font class="Apple-style-span" color="#1306b1"><br></font></div><div><font class="Apple-style-span" color="#1306b1">Etomo takes care of the second two steps at once with the “Generate Course Aligned Stack” button.</font></div><div><font class="Apple-style-span" color="#1306b1"><br></font></div><div><font class="Apple-style-span" color="#1306b1">If you want to try to get better initial automated alignment, it may be worth trying any (combination) of the following:</font></div><div><font class="Apple-style-span" color="#1306b1">in the advanced tab: </font></div><div><font class="Apple-style-span" color="#1306b1">Click Exclude central peak</font></div><div><font class="Apple-style-span" color="#1306b1">Change frequencies used</font></div><div><font class="Apple-style-span" color="#1306b1">Try No Cosine Stretch</font></div><div><font class="Apple-style-span" color="#1306b1">Try Cumulative correlation</font></div><div><font class="Apple-style-span" color="#1306b1"><br></font></div><div><font class="Apple-style-span" color="#1306b1">I’ve had some luck with some of these in the past, but it does depend on your data set.</font></div></span><br class="Apple-interchange-newline"></blockquote></div>Hi Ariane, Huy, Lu, & Mike,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Thanks for your responses. I think my error was rerunning the cross-correlations. I put in Mike's response, since it was the most complete. Thanks also for the suggestion of the IMOD list; I didn't know there was one.<br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><span class="Apple-tab-span" style="white-space: pre; "> </span>Yours,</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>Bill</div><div><br></div></div></span><br class="Apple-interchange-newline"> </div><br></div></body></html>