https://megcore.nih.gov/index.php?action=history&feed=atom&title=Troubleshooting%3A_Analysis_Topics 2026-04-07T10:46:32Z Revision history for this page on the wiki MediaWiki 1.44.2 https://megcore.nih.gov/index.php?title=Troubleshooting:_Analysis_Topics&diff=5652&oldid=prev 2024-04-24T18:53:40Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 14:53, 24 April 2024</td> </tr><tr> <td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td> </tr> <tr> <td class="diff-marker" data-marker="−"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>''Under Construction''</div></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">'''</ins>''Under Construction<ins style="font-weight: bold; text-decoration: none;">'''</ins>''</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt;</div></td> </tr> <tr> <td colspan="2" class="diff-empty diff-side-deleted"></td> <td class="diff-marker" data-marker="+"></td> <td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>''Collection of analysis tips/troubleshooting discovered during process. This page is primarily a temporary holding space until these notes can be filed in the proper sections.''</div></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br /></td> </tr> <tr> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Freesurfer - BEM creation==</div></td> <td class="diff-marker"></td> <td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Freesurfer - BEM creation==</div></td> </tr> </table>

Amnamyst https://megcore.nih.gov/index.php?title=Troubleshooting:_Analysis_Topics&diff=5651&oldid=prev 2024-04-24T18:52:01Z

<p>Created page with &quot;&#039;&#039;Under Construction&#039;&#039; ==Freesurfer - BEM creation== *BOTH FreeSurfer recon-all -autorecon1 and mne.make_watershed_bem independently call mri_watershed to produce a skull-stripped image from which the inner and outer skull surfaces are created. *The use of -gcaatlas ensures that the bem will pick up the cerebellum, and doesn&#039;t clip out other portions of the brain. *In some cases, -gcaatlas worsens a bem that was already bad but not catastrophic. (i.e. it included some...&quot;</p> <p><b>New page</b></p><div>&#039;&#039;Under Construction&#039;&#039;<br /> <br /> ==Freesurfer - BEM creation==<br /> <br /> *BOTH FreeSurfer recon-all -autorecon1 and mne.make_watershed_bem independently call mri_watershed to produce a skull-stripped image from which the inner and outer skull surfaces are created.<br /> *The use of -gcaatlas ensures that the bem will pick up the cerebellum, and doesn&#039;t clip out other portions of the brain.<br /> *In some cases, -gcaatlas worsens a bem that was already bad but not catastrophic. (i.e. it included some curlicues but didn&#039;t crop out any of the brain). This is usually the result of a bad skullstrip, and can be fixed by lowering the default preflood height from 30 to 15, 10, or even 5.<br /> *In very rare cases, -gcaatlas results in a worse skullstrip. (*Observed in subject with Dx.)<br /> <br /> &#039;&#039;&#039;Recommended course of action&#039;&#039;&#039; is to use -gcaatlas, but check all bems and change preflood height as necessary.<br /> <br /> The use of -gcaatlas does actually improve matters for many subjects, eliminating cropping off of brain structures. Occasionally, using -gcaatlas results in failure, this again is usually a sign that the bem was already weird even without -gcaatlas<br /> <br /> &#039;&#039;&#039;For ENIGMA, recommended course of action:&#039;&#039;&#039; <br /> * Keep -gcaatlas implementation<br /> * Manually run several participants with bem failures and adjust preflood height on mri_watershed/make_watershed_bem<br /> * Inspect output errors for any remaining &quot;no vertices&quot; errors that are potentially due to a bad skullstrip</div>

Amnamyst