{"id":96,"date":"2020-11-07T03:32:06","date_gmt":"2020-11-06T18:32:06","guid":{"rendered":"http:\/\/nshalnote.com\/?p=96"},"modified":"2022-12-12T11:42:19","modified_gmt":"2022-12-12T02:42:19","slug":"%e3%80%90freeview%e2%91%a0%e3%80%91freesurfer%e3%82%a4%e3%83%b3%e3%82%b9%e3%83%88%e3%83%bc%e3%83%ab%e5%be%8c%e3%81%ab%e8%a1%8c%e3%81%86%e3%81%b9%e3%81%8d%e3%81%93%e3%81%a8-2","status":"publish","type":"post","link":"https:\/\/nshalnote.com\/%e3%80%90freeview%e2%91%a0%e3%80%91freesurfer%e3%82%a4%e3%83%b3%e3%82%b9%e3%83%88%e3%83%bc%e3%83%ab%e5%be%8c%e3%81%ab%e8%a1%8c%e3%81%86%e3%81%b9%e3%81%8d%e3%81%93%e3%81%a8-2\/","title":{"rendered":"\u3010FreeView\u3011FreeSurfer\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u5f8c\u306b\u884c\u3046\u3079\u304d\u3053\u3068 #2"},"content":{"rendered":"\n

\u524d\u30da\u30fc\u30b8\uff1a\u3010Recon-all\u3011FreeSurfer\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u5f8c\u306b\u884c\u3046\u3079\u304d\u3053\u3068 #1<\/a><\/p>\n\n\n\n

\u524d\u56de\u3001FreeSurfer\u3092\u7528\u3044\u3066MRI\u30c7\u30fc\u30bf\u306b Recon-all\u30b3\u30de\u30f3\u30c9\u3092\u7528\u3044\u3066Subject\u3092\u4f5c\u6210\u3067\u304d\u305f\u3068\u601d\u3044\u307e\u3059\u3002
\u4eca\u56de\u306fSubject\u306e\u5185\u5bb9\u3092\u78ba\u8a8d\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002\u78ba\u8a8d\u306b\u306fFreeview<\/span><\/span>\u3068\u3044\u3046GUI\u3092\u7528\u3044\u307e\u3059\u3002

\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3067\u8aad\u307f\u8fbc\u307f\u307e\u3059\u3002
\u3053\u306e\u30b3\u30de\u30f3\u30c9\u306fRecon-all\u304c\u554f\u984c\u306a\u304f\u51e6\u7406\u3067\u304d\u305f\u304b\u78ba\u8a8d\u3059\u308b\u969b\u3001\u57fa\u672c\u3068\u306a\u308b\u30de\u30b9\u30af\u753b\u50cf\u306e\u7d44\u307f\u5408\u308f\u305b\u3092\u8868\u3057\u3066\u3044\u307e\u3059\u3002<\/p>\n\n\n\n

cd $SUBJECTS_DIR
freeview -v \\
test001\/mri\/T1.mgz \\
test001\/mri\/wm.mgz \\
test001\/mri\/brainmask.mgz \\
test001\/mri\/aseg.mgz:colormap=lut:opacity=0.2 \\
-f \\
test001\/surf\/lh.white:edgecolor=blue \\
test001\/surf\/lh.pial:edgecolor=red \\
test001\/surf\/rh.white:edgecolor=blue \\
test001\/surf\/rh.pial:edgecolor=red<\/p>\n\n\n\n

[ test001 ]<\/span><\/span>\u306e\u7b87\u6240\u306b\u81ea\u8eab\u3067\u8a2d\u5b9a\u3057\u305f Subject\u540d<\/span><\/span>\u3092\u5165\u529b\u3057\u3066\u304f\u3060\u3055\u3044\u3002
Recon-all\u304c\u554f\u984c\u306a\u304f\u884c\u3048\u3066\u3044\u308c\u3070\u4e0b\u8a18\u306e\u3088\u3046\u306a\u30a6\u30a3\u30f3\u30c9\u30a6\u304c\u7acb\u3061\u4e0a\u304c\u308a\u307e\u3059\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u5de6\u4e0a\u306e\u30c1\u30a7\u30c3\u30af\u30dc\u30c3\u30af\u30b9\u3092\u78ba\u8a8d\u3057\u3066\u304f\u3060\u3055\u3044\u3002
[ Volumes ]<\/span> \u306f\u76ae\u8cea\u4e0b\u69cb\u9020\u3092Segmentation\u3057\u305f\u30de\u30b9\u30af\u753b\u50cf\u3092\u91cd\u306d\u5408\u308f\u305b\u305f\u3082\u306e\u3001
[ Surface ]<\/span> \u306f\u7070\u767d\u8cea\u3068\u767d\u8cea\u3092\u8a2d\u5b9a\u3057\u3066\u304a\u308a\u3001\u76ae\u8cea\u69cb\u9020\u3092\u518d\u69cb\u6210\u3057\u305f\u3082\u306e\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n

\u8a66\u3057\u306b[ Surface ] \u306e\u30c1\u30a7\u30c3\u30af\u30dc\u30c3\u30af\u30b9\u3092\u5168\u3066\u5916\u3057\u305f\u72b6\u614b\u306b\u3057\u3066\u304f\u3060\u3055\u3044\u3002
\u76ae\u8cea\u4e0b\u69cb\u9020\u3054\u3068\u306b\u8272\u5206\u3051\u3055\u308c\u3066\u304a\u308a\u3001Segmantation<\/span>\u304c\u554f\u984c\u306a\u3044\u304b\u78ba\u8a8d\u3067\u304d\u307e\u3059\u3002
\u4e0b\u8a18\u753b\u50cf\u3067\u306fRight-Putamen\u3092\u9078\u629e\u3057\u3066\u3044\u307e\u3059\u3002<\/p>\n\n\n

\n
\"\"<\/figure>\n<\/div>\n\n\n

\u6b21\u306b[ Surface ]<\/span>\u306e\u30c1\u30a7\u30c3\u30af\u3092\u5168\u3066\u623b\u3057\u307e\u3059\u3002
Recon-all\u306b\u3088\u308b\u524d\u51e6\u7406\uff08\u7279\u306bSkull-strip)\u304c\u554f\u984c\u306a\u304f\u884c\u3048\u305f\u304b\u78ba\u8a8d\u3057\u307e\u3057\u3087\u3046\u3002
\u6b8b\u3063\u3066\u3057\u307e\u3063\u305f\u9aa8\u30fb\u786c\u819c\u304c\u7070\u767d\u8cea\u3068\u3057\u3066\u30ab\u30a6\u30f3\u30c8\u3055\u308c\u3066\u3044\u308b\u5834\u5408\u3001\u305d\u306e\u90e8\u5206\u306e\u4fee\u6b63\u304c\u5fc5\u8981\u3067\u3059\u3002<\/p>\n\n\n\n

\u4f59\u5206\u306b\u30ab\u30a6\u30f3\u30c8\u3055\u308c\u3066\u3044\u308b\u90e8\u5206\u306f GUI \u5de6\u4e0a\u306e [ R ] \u3092\u30af\u30ea\u30c3\u30af\u3057\u3001
Shift + Command +\u5de6\u30af\u30ea\u30c3\u30af \u3092\u62bc\u3057\u305f\u307e\u307e\u30c9\u30e9\u30c3\u30b0\u3059\u308b<\/span>\u3068\u524a\u9664\u3059\u308b\u3053\u3068\u304c\u3067\u304d\u307e\u3059\u3002<\/p>\n\n\n

\n
\"\"<\/figure>\n<\/div>\n\n\n

\u4f59\u5206\u306a\u90e8\u5206\u3092\u524a\u9664\u3057\u305f\u5f8c\u306b\u30d5\u30a1\u30a4\u30eb > Save Volume \u53ca\u3073 Save Surface\u3092\u9078\u629e\u3057\u7d42\u4e86\u3057\u307e\u3059\u3002
\u305d\u306e\u5f8c\u3001\u4e0b\u8a18\u306e\u30b3\u30de\u30f3\u30c9\u3092\u5165\u529b\u3059\u308b\u3053\u3068\u3067 Subject \u3092\u66f4\u65b0\u3067\u304d\u307e\u3059\u3002<\/p>\n\n\n\n

recon-all -s test001 -autorecon-pial<\/p>\n\n\n\n

recon-all -s\u3010Subject\u540d\u3011 -autorecon-pial<\/p>\n\n\n\n

\u518d\u5ea6 Freeview\u3092\u958b\u3044\u3066Recon-all \u5f8c\u306e\u30c7\u30fc\u30bf\u304c\u6b63\u3057\u304f\u524d\u51e6\u7406\u3055\u308c\u3066\u3044\u308b\u304b\u78ba\u8a8d\u3057\u3066\u304f\u3060\u3055\u3044\u3002
\u3053\u308c\u3067\u5927\u307e\u304b\u306a\u524d\u51e6\u7406\u306e\u30c1\u30a7\u30c3\u30af\u306f\u7d42\u4e86\u3067\u3059\u3002\u6b21\u306f\u76ae\u8cea\u306eParcellation\u306e\u78ba\u8a8d\u3067\u3059\u3002<\/p>\n\n\n\n

Next\uff1a\u3010FreeView\u3011FreeSurfer\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u5f8c\u306b\u884c\u3046\u3079\u304d\u3053\u3068 #3<\/a><\/p>\n\n\n

\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\u3042\u308f\u305b\u3066\u8aad\u307f\u305f\u3044<\/span>\n\t\t\t\t\t
\"\"<\/figure><\/div>\t\t\t\t\t
\n\t\t\t\t\t\t\u3010FreeView\u3011FreeSurfer\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u5f8c\u306b\u884c\u3046\u3079\u304d\u3053\u3068 #3<\/a>\n\t\t\t\t\t\t\u524d\u30da\u30fc\u30b8\uff1a\u3010FreeView\u2460\u3011FreeSurfer\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u5f8c\u306b\u884c\u3046\u3079\u304d\u3053\u3068 #2 \u524d\u56de\u306f Recon-all \u5f8c\u306e Subject \u304c\u6b63\u78ba\u306b\u524d\u51e6\u7406\u3067\u304d\u3066\u3044\u308b\u304b\u3001freeview\u3092\u7528\u3044\u3066\u78ba\u8a8d\u3057\u307e\u3057\u305f\u3002\u4eca\u56de…<\/span>\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t<\/div>","protected":false},"excerpt":{"rendered":"

\u524d\u30da\u30fc\u30b8\uff1a\u3010Recon-all\u3011FreeSurfer\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u5f8c\u306b\u884c\u3046\u3079\u304d\u3053\u3068 #1 \u524d\u56de\u3001FreeSurfer\u3092\u7528\u3044\u3066MRI\u30c7\u30fc\u30bf\u306b Recon-all\u30b3\u30de\u30f3\u30c9\u3092\u7528\u3044\u3066Subject\u3092\u4f5c\u6210\u3067\u304d\u305f\u3068\u601d\u3044\u307e\u3059\u3002\u4eca\u56de\u306fSu […]<\/p>\n","protected":false},"author":1,"featured_media":715,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"swell_btn_cv_data":"","footnotes":""},"categories":[2,96],"tags":[26,9,11,10,27,17,24,25],"class_list":["post-96","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-freesurfer","category-image-analysis","tag-autorecon","tag-freesurfer","tag-freeview","tag-mri","tag-pial","tag-recon-all","tag-surface","tag-volume"],"_links":{"self":[{"href":"https:\/\/nshalnote.com\/wp-json\/wp\/v2\/posts\/96","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/nshalnote.com\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/nshalnote.com\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/nshalnote.com\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/nshalnote.com\/wp-json\/wp\/v2\/comments?post=96"}],"version-history":[{"count":10,"href":"https:\/\/nshalnote.com\/wp-json\/wp\/v2\/posts\/96\/revisions"}],"predecessor-version":[{"id":716,"href":"https:\/\/nshalnote.com\/wp-json\/wp\/v2\/posts\/96\/revisions\/716"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/nshalnote.com\/wp-json\/wp\/v2\/media\/715"}],"wp:attachment":[{"href":"https:\/\/nshalnote.com\/wp-json\/wp\/v2\/media?parent=96"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/nshalnote.com\/wp-json\/wp\/v2\/categories?post=96"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/nshalnote.com\/wp-json\/wp\/v2\/tags?post=96"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}