Tutorials fot surfaces

ICEM笔记目录目录...................................................................... (1)1 入门介绍...................................................................... (3)1.1 ICEM保存时各个文件类型的含义 ..................................................................... (3)1.1.1 ICEM在画网格时保存注意事项 (4)1.1.2 几何导入ICEM时，如何在ICEM中设置精度, (4)1.1.3 如何生成rpl文件 ..................................................................... . (4)1.1.4 如何将Pro/E生成的几何导入到ICEM中, (4)1.1.5 在PRO/E中如何生成二维平面几何，导入到ICEM中, (5)1.1.6 PRO/E中装配体如何进行划分网格, (5)1.2 ICEM中对于结构化网格与块的映射的思考 (5)2Geometriy .............................................................. (6)2.1 Geometry概念及用处简介 ..................................................................... .. (7)2.1.1 辅助点、辅助线、辅助面的必要性 (7)2.1.2 ICEM或PRO/E建立几何，需要建立拓扑的必要性。

(7)2.2 CreatePoint .................................................................. ............................................. 7 2.3 Create Modify Curve................................................................... (8)2.3.1 前面几种生成曲线的简单方式 (8)2.3.2 Isocurve Method.................................................................. .. (8)2.3.3 Surface-SurfaceIntersection ........................................................... .. (9)2.3.4 Project Curve on Surface................................................................. .. (9)2.3.5 Concatenate/ReapproximateCurves (9)2.3.6 Extract Curves fromSurfaces ............................................................... .. (9)2.3.7 ModifyCurves ................................................................. .. (9)2.3.8 CreateMidline ................................................................ ............................. 10 2.4 Create/ModifySurface ................................................................ . (10)2.4.1 From Curves选项 ..................................................................... (10)2.4.2 Curve Driven选项 ..................................................................... .. (10)2.4.3 Sweep Surface选项 ..................................................................... (10)2.4.4 Loft Surface over SeveralCurves ...............................................................102.4.5 Midsurface选项...................................................................... .. (11)2.4.6 Segment/TrimSurface ................................................................ .. (11)2.4.7 Create Curtain Surface、Extend Surface、GeometrySimplification (11)2.4.8 StandardShapes ................................................................. ......................... 11 2.5 RepairGeometry ............................................................... .. (12)2.5.1 BuildTopology ............................................................... .. (12)3Mesh ................................................................... .. (12)3.1 一般性问题 ..................................................................... . (13)3.1.1 有时候将边界层设置很薄时，会出现负体积，若将第一层厚度社大写，则有变成正体积了。

皮层厚度和表面积（surface area）——Freesurfer分析方法预备阶段：1打开终端，输入指令，打开tschtcshsetenv FREESURFER_HOME /usr/local/freesurfersource $FREESURFER_HOME/SetUpFreeSurfer.cshsetenv TUTORIAL_DATA /media/8498B05D98B05002/DATA/fs-cyh setenv SUBJECTS_DIR $TUTORIAL_DATAcd $SUBJECTS_DIR2Recon-allrecon-all \-i <one slice in the anatomical dicom series> \-s <subject id that you make up> \-sd <directory to put the subject folder in> \-allrecon-all -i 66540045 -s study -all文件文件夹名配准tkregister2 --mgz --s study1 --fstal --surf orig查看看分割结果tkmedit cyh brainmask.mgz -aux T1.mgz -surfs -aseg看膨胀结果tksurfer cyh lh inflated在Freesurfer中，经过recon-all指令预处理，一些统计数据已经产生。

他们保存在每个被试的stas/子文件夹下。

有subcortical segmentation (aseg)皮层下组织分割的，还有 cortical parcellation (aparc)皮层分割的结果。

一、单被试分析（1）通过上面的命令行可以得到Structure Name, Number of Vertices, Surface Area, Gray Matter Volume, Average Thickness,Thickness StDev, Integrated Rectified Mean Curvature, Integrated Rectified Gaussian Curvature, Folding Index and Intrinsic Curvature Index for each entry in the table.（2）要得到某个指定区域的统计信息，可参照Q. I am trying to measure the cortical thickness of specific ROI, how can I do this?A: You can save the ROI to a label file and then use:•mris_anatomical_stats -l <label file>（3）要计算全脑平均厚度，参照Q. I am trying to measure the global mean cortical thickness (i.e combined across hemispheres), how would I do this?A: One suggestion is to use the surface area of each hemisphere as the weighting factor. In which case the global mean thickness including both hemispheres would be given by:bh.thickness = ( (lh.thickness * lh.surfarea) + (rh.thickness * rh.surfarea) ) / (lh.surfarea +rh.surfarea)If you use the values in the ?h.aparc.stats, it already factors out the 'unknown' region, so you don't have to do it yourself.皮层下组织的统计数据cd $SUBJECTS_DIR/004/statsThings to do:1.You can load the table into a spreadsheet as explained in the previous section.2.Refer to the file FreeSurferColorLUT.txt for the segmentation labels and thecorresponding subcortical structures.Things to do:1.You can load the table into a spreadsheet.2.Refer to the file FreeSurferColorLUT.txt for the segmentation labels and thecorresponding subcortical structures.Cortical Thickness of a Volume-defined ROIThis page describes the workflow to extract freesurfer cortical thickness values for a region-of-interest (ROI) defined in volume space.从freesurfer分析结果里提取出ROI的皮层厚度。

Package‘rmdformats’October14,2022Maintainer Julien Barnier<**********************>Version1.0.4Date2022-05-10License GPL(>=2)Encoding UTF-8Title HTML Output Formats and Templates for'rmarkdown'DocumentsDescription HTML formats and templates for'rmarkdown'documents,with some extra features such as automatic table of contents,lightboxedfigures,dynamiccrosstab helper.Imports knitr,rmarkdown,bookdown,htmltoolsSuggests questionr,DT,palmerpenguins,ggplot2URL https:///juba/rmdformatsBugReports https:///juba/rmdformats/issuesRoxygenNote7.1.2NeedsCompilation noAuthor Julien Barnier[aut,cre]Repository CRANDate/Publication2022-05-1708:50:03UTCR topics documented:downcute (2)html_clean (3)html_docco (4)lockdown (6)material (6)pilltabs (7)print.pilltabs (8)readthedown (9)robobook (10)Index1212downcute downcute Convert to an HTML documentDescriptionFormat for converting from R Markdown to an HTML document.Usagedowncute(fig_width=8,fig_height=5,fig_caption=TRUE,lightbox=FALSE,thumbnails=FALSE,gallery=FALSE,toc_depth=2,embed_fonts=TRUE,use_bookdown=FALSE,pandoc_args=NULL,md_extensions=NULL,mathjax="rmdformats",highlight=NULL,default_style=c("light","dark"),downcute_theme=c("default","chaos"),...)Argumentsfig_width Default width(in inches)forfiguresfig_height Default width(in inches)forfiguresfig_caption TRUE to renderfigures with captionslightbox if TRUE,add lightbox effect to content imagesthumbnails if TRUE display content images as thumbnailsgallery if TRUE and lightbox is TRUE,add a gallery navigation between images in lightbox displaytoc_depth adjust table of contents depthembed_fonts if TRUE,use localfiles for fonts used in the template.This leads to biggerfiles but ensures that these fonts are available.If FALSE they are downloaded fromGoogle Web Fonts.use_bookdown if TRUE,uses html_document2instead of html_document,thus providing num-bered sections and cross referencespandoc_args arguments passed to the pandoc_args argument of rmarkdown html_documenthtml_clean3md_extensions arguments passed to the md_extensions argument of rmarkdown html_document mathjax set to NULL to disable Mathjax insertionhighlight syntax highlighting,forced to NULL as highlighting is done via prism.jsdefault_style specify default display style,"light"or"dark"downcute_theme document template theme...Additional function arguments passed to R Markdown html_document DetailsCSS taken from the docute project and adaptations made by John Coene.Please note that as syntax highlighting is done with the Prism JavaScript library,using the‘highlight‘argument here will have no effect.ValueR Markdown output format to pass to renderhtml_clean Convert to an HTML documentDescriptionFormat for converting from R Markdown to an HTML document.Usagehtml_clean(fig_width=6,fig_height=6,fig_caption=TRUE,highlight="kate",lightbox=TRUE,thumbnails=TRUE,gallery=FALSE,toc=TRUE,toc_depth=2,use_bookdown=FALSE,pandoc_args=NULL,md_extensions=NULL,mathjax="rmdformats",...)Argumentsfig_width Default width(in inches)forfiguresfig_height Default width(in inches)forfiguresfig_caption TRUE to renderfigures with captionshighlight Syntax highlighting style.Supported styles include"default","tango","pyg-ments","kate","monochrome","espresso","zenburn","haddock",and"text-mate".Pass NULL to prevent syntax highlighting.lightbox if TRUE,add lightbox effect to content imagesthumbnails if TRUE display content images as thumbnailsgallery if TRUE and lightbox is TRUE,add a gallery navigation between images in lightbox displaytoc if TRUE,display a table of contentstoc_depth adjust table of contents depthuse_bookdown if TRUE,uses html_document2instead of html_document,thus providing num-bered sections and cross referencespandoc_args arguments passed to the pandoc_args argument of rmarkdown html_document md_extensions arguments passed to the md_extensions argument of rmarkdown html_document mathjax set to NULL to disable Mathjax insertion...Additional function arguments passed to R Markdown html_document DetailsStyling and features are very similar to the ones from the great knitrBootstrap package by Jim Hester :https:///jimhester/knitrBootstrapValueR Markdown output format to pass to renderhtml_docco Convert to an HTML documentDescriptionFormat for converting from R Markdown to an HTML document.Usagehtml_docco(fig_width=6,fig_height=6,fig_caption=TRUE,highlight="kate",lightbox=TRUE,thumbnails=TRUE,gallery=FALSE,use_bookdown=FALSE,pandoc_args=NULL,md_extensions=NULL,mathjax="rmdformats",...)Argumentsfig_width Default width(in inches)forfiguresfig_height Default width(in inches)forfiguresfig_caption TRUE to renderfigures with captionshighlight Syntax highlighting style.Supported styles include"default","tango","pyg-ments","kate","monochrome","espresso","zenburn","haddock",and"text-mate".Pass NULL to prevent syntax highlighting.lightbox if TRUE,add lightbox effect to content imagesthumbnails if TRUE display content images as thumbnailsgallery if TRUE and lightbox is TRUE,add a gallery navigation between images in lightbox displayuse_bookdown if TRUE,uses html_document2instead of html_document,thus providing num-bered sections and cross referencespandoc_args arguments passed to the pandoc_args argument of rmarkdown html_document md_extensions arguments passed to the md_extensions argument of rmarkdown html_document mathjax set to NULL to disable Mathjax insertion...Additional function arguments passed to rmarkdown html_documentDetailsThe CSS is heavily inspired from the default one of the docco project:https:/// docco/.ValueR Markdown output format to pass to render6material lockdown Convert to an HTML documentDescriptionFormat for converting from R Markdown to an HTML document.Usagelockdown(...)Arguments...Additional function arguments passed to R Markdown html_document DetailsTODOValueR Markdown output format to pass to rendermaterial Material design-bootstrap HTML output formatDescriptionFormat for converting from R Markdown to an HTML document with a material design theme.Usagematerial(fig_width=6,fig_height=6,fig_caption=TRUE,highlight="kate",lightbox=TRUE,thumbnails=TRUE,gallery=FALSE,cards=TRUE,use_bookdown=FALSE,pandoc_args=NULL,md_extensions=NULL,mathjax="rmdformats",...)pilltabs7 Argumentsfig_width Default width(in inches)forfiguresfig_height Default width(in inches)forfiguresfig_caption TRUE to renderfigures with captionshighlight Syntax highlighting style.Supported styles include"default","tango","pyg-ments","kate","monochrome","espresso","zenburn","haddock",and"text-mate".Pass NULL to prevent syntax highlighting.lightbox if TRUE,add lightbox effect to content imagesthumbnails if TRUE display content images as thumbnailsgallery if TRUE and lightbox is TRUE,add a gallery navigation between images in lightbox displaycards if TRUE,sections will be presented as distinct and animated cardsuse_bookdown if TRUE,uses html_document2instead of html_document,thus providing num-bered sections and cross referencespandoc_args arguments passed to the pandoc_args argument of rmarkdown html_document md_extensions arguments passed to the md_extensions argument of rmarkdown html_document mathjax set to NULL to disable Mathjax insertion...Additional function arguments passed to R Markdown html_documentDetailsJavaScript and CSS taken and adapted from the Material design theme for Bootstrap3project: https:///FezVrasta/bootstrap-material-design.ValueR Markdown output format to pass to renderpilltabs Given a cross-table,outputs HTML code to display several views ofwith a tabbed interfaceDescriptionGiven a two dimensions contingency table,this function outputs HTML code to display,within a dynamic tabbed interface,the count,row percentages,column percentages and chi-squared residu-als tables.8print.pilltabsUsagepilltabs(tab,count=TRUE,rows=TRUE,cols=TRUE,chisq=TRUE,resid=TRUE,s=TRUE)Argumentstab a two dimensions table objectcount whether or not to display the count tablerows whether or not to display the row percentages tablecols whether or not to display the column percentages tablechisq whether or not to display the table chi-squared test resultsresid whether or not to display the chi-squared residuals tables whether or not to display the table row namesDetailsThe function is intended to be called inside an rmarkdown document.ValueNo value is returned.Examplesdata(airquality)tab<-table(airquality$Month,airquality$Ozone>25)pilltabs(tab)print.pilltabs Printing functions for pilltabsDescriptionNot to be used directlyreadthedown9Usage##S3method for class pilltabsprint(x,...)##S3method for class pilltabsknit_print(x,...)Argumentsx data to be printed,generated by pilltabs...arguments passed to other methodsreadthedown Convert to an HTML documentDescriptionFormat for converting from R Markdown to an HTML document.Usagereadthedown(fig_width=8,fig_height=5,fig_caption=TRUE,highlight="kate",lightbox=FALSE,thumbnails=FALSE,gallery=FALSE,toc_depth=2,embed_fonts=TRUE,use_bookdown=FALSE,pandoc_args=NULL,md_extensions=NULL,mathjax="rmdformats",...)Argumentsfig_width Default width(in inches)forfiguresfig_height Default width(in inches)forfiguresfig_caption TRUE to renderfigures with captionshighlight Syntax highlighting style.Supported styles include"default","tango","pyg-ments","kate","monochrome","espresso","zenburn","haddock",and"text-mate".Pass NULL to prevent syntax highlighting.10robobook lightbox if TRUE,add lightbox effect to content imagesthumbnails if TRUE display content images as thumbnailsgallery if TRUE and lightbox is TRUE,add a gallery navigation between images in lightbox displaytoc_depth adjust table of contents depthembed_fonts if TRUE,use localfiles for fonts used in the template.This leads to biggerfiles but ensures that these fonts are available.If FALSE they are downloaded fromGoogle Web Fonts.use_bookdown if TRUE,uses html_document2instead of html_document,thus providing num-bered sections and cross referencespandoc_args arguments passed to the pandoc_args argument of rmarkdown html_document md_extensions arguments passed to the md_extensions argument of rmarkdown html_document mathjax set to NULL to disable Mathjax insertion...Additional function arguments passed to R Markdown html_documentDetailsCSS adapted from the readtheorg theme of the org-html-themes project:https:/// fniessen/org-html-themes,which is itself inspired by the Read the docs theme:https:// /.ValueR Markdown output format to pass to renderrobobook Convert to an HTML documentDescriptionFormat for converting from R Markdown to an HTML document.Usagerobobook(fig_width=8,fig_height=5,fig_caption=TRUE,highlight="kate",lightbox=FALSE,thumbnails=FALSE,gallery=FALSE,toc_depth=2,embed_fonts=TRUE,use_bookdown=FALSE,robobook11 pandoc_args=NULL,md_extensions=NULL,mathjax="rmdformats",...)Argumentsfig_width Default width(in inches)forfiguresfig_height Default width(in inches)forfiguresfig_caption TRUE to renderfigures with captionshighlight Syntax highlighting style.Supported styles include"default","tango","pyg-ments","kate","monochrome","espresso","zenburn","haddock",and"text-mate".Pass NULL to prevent syntax highlighting.lightbox if TRUE,add lightbox effect to content imagesthumbnails if TRUE display content images as thumbnailsgallery if TRUE and lightbox is TRUE,add a gallery navigation between images in lightbox displaytoc_depth adjust table of contents depthembed_fonts if TRUE,use localfiles for fonts used in the template.This leads to biggerfiles but ensures that these fonts are available.If FALSE they are downloaded fromGoogle Web Fonts.use_bookdown if TRUE,uses html_document2instead of html_document,thus providing num-bered sections and cross referencespandoc_args arguments passed to the pandoc_args argument of rmarkdown html_document md_extensions arguments passed to the md_extensions argument of rmarkdown html_document mathjax set to NULL to disable Mathjax insertion...Additional function arguments passed to R Markdown html_document DetailsCSS adapted from the bookdown project,with Roboto family fonts.ValueR Markdown output format to pass to renderIndexdowncute,2html_clean,3html_docco,4html_document,2–7,10,11html_document2,2,4,5,7,10,11knit_print.pilltabs(print.pilltabs),8 lockdown,6material,6pilltabs,7,9print.pilltabs,8readthedown,9render,3–7,10,11robobook,1012。

PySide TutorialsIn this wiki page, we have sorted out some tutorials structured by rough experience levels. So we have tutorials for absolute beginners, for intermediate#调解，中间，中级 PySide developers and for the more advanced ones who are just searching for simple solutions for their complex problems.Beginner tutorials⇧Your first PySide application – A simple Hello World application.⇧A simple clickable button tutorial – Clickable button which will show Hello World each time you press it.⇧Simple PySide dialog application – Creates a simple dialog with an edit area and a button to greet the user.⇧pyside-simplicissimus – 10 minutes newbie to newbie code snippets.Advanced tutorials⇧Hatchet: hack frozen PySide apps down to size [rfk.id.au]Your first PySide applicationIf you followed Setting up PySide wiki page to install PySide, you should now have a full blown copy of PySide on your machine to start developing Qt+Python GUI applications. As any other programming framework, you start by the traditional “Hello World”.Here is a simple example of an Hello World in PySide:1 2 3 4 5 #!/usr/bin/python# Import PySide classes import sysfrom PySide.QtCore import *6 7 8 9 10 11 12 13 14 15 16 from PySide.QtGui import *# Create a Qt applicationapp = QApplication(sys.argv)# Create a Label and show itlabel = QLabel("Hello World")label.show()# Enter Qt application main loopapp.exec_()sys.exit()With PySide desktop applications, you must always start your file by importing PySide.QtCore and PySide.QtGui classes. These classes have the main functions for building PySide applications. For instance, PySide.QtGui contains functions for dealing with widgets while PySide.QtCore contains methods for handling signals and slots, and controlling the application.After the imports, you create a QApplication which is the main Qt application. As Qt can receive arguments from command line, you must pass any arguments to the QApplication obje ct. Usually, you don’t need to pass any arguments so you can leave it as it is.After the creation of the application object, we have created a QLabel object. A QLabel is a widget that can present text (simple or rich, like html), and images. Note that after the creation of the label, we are calling the method show which will present the label to the user.Finally, we call app.exec_() which will enter the Qt main loop and start to execute the Qt code. In reality, it is only here that the label will be shown, but this can be ignored for now.Displaying html in the labelAs mentioned previously, you can insert html tags in the label to present rich text. Try changing the code which creates the label for something like:label = QLabel("<font color=red size=40>Hello World</font>")#就是用htmltag 指定 str 样式and you will the the “Hello World” now bigger and red. You can try to change to another color, another size, or make it blink! Or you can create other elements instead of the QLabel, like QPushButton, or others. PySide 教程：第一个PySide 应用使用你已经安装了PySide,那么现在你应该已经拥有完整的PySide拷贝，并且可以使用Qt+Python的方式开发GUI应用程序。