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  1. %----------------------------------------------------------------------------------
  2. % (c) 2018 Hennadii Madan, using as a template a thesis
  3. % (c) 2006,2007 Tomaz Vrtovec
  4. % PhD Thesis
  5. %----------------------------------------------------------------------------------
  6.  
  7. %--------------------------
  8. % define document style: A4 paper size, two-sided printing, 12pt font, report style
  9. documentclass[a4paper,twoside,12pt]{report}
  10. %--------------------------
  11. % WARN ABOUT OBSOLETE PACKAGES (Oh, latex)
  12. usepackage{nag}
  13. %--------------------------
  14. % declare common packages
  15. usepackage[slovene,british]{babel}
  16. usepackage[utf8]{inputenc} %It is necessary to do the import with utf8 beacuse
  17. inputencoding{cp1250} %of the way inputenc works: for unicode but not
  18. %other encodings is scans the files for the
  19. %characters that are actually used and applies the
  20. %settings only for them. So I import with utf8 but
  21. %then immediately switch to cp1250 for the code
  22. %written by Tomaz.
  23.  
  24. usepackage[pdftex]{graphicx}
  25. %usepackage[pdftex,draft]{graphicx} %remove draft for images!!!!
  26. usepackage{verbatim}
  27. usepackage{eso-pic}
  28. % usepackage{color}
  29. usepackage{amsmath}
  30. usepackage{amssymb}
  31. usepackage{enumitem}
  32. usepackage{dsfont}
  33. usepackage{multirow}
  34. usepackage{txfonts}
  35.  
  36. % page dimensions (A4 = 8.5in x 11.0in)
  37. setlength{textwidth}{6.3in} % width of text area (= 8.5in - 2*1.1in)
  38. setlength{textheight}{9.0in} % height of text area (= 11.0in - 2*1.0in)
  39. setlength{topmargin}{0.0in} % for top margin of 1.0in
  40. setlength{headheight}{0.7in} % height of the head area
  41. setlength{headsep}{0.5in} % separationbetween text and header
  42. setlength{voffset}{-1.0in} % vertical offset
  43. setlength{footskip}{1.0in} % baseline-baseline distance between footline and last line of text
  44. setlength{oddsidemargin}{0.2in} % side margin on odd pages
  45. setlength{evensidemargin}{-0.1in} % side margin on even pages
  46. raggedbottom % no extra vertical space is added to pages
  47. % paragraph settings
  48. setlength{parindent}{0.0in} % indentation of paragraphs
  49. setlength{parskip}{0.0em} % set vertical space between paragraphs
  50.  
  51. %?? hyphenation settings
  52. %hyphenpenalty=5000
  53. %tolerance=1000
  54.  
  55. % disable overfull hbox warnings ?? (sloppy vs. fussy)
  56. sloppy
  57.  
  58. % fonts (packages: mathdesign, concrete, mathpazo or none for cm default font)
  59. %usepackage[garamond]{mathdesign} % font: Garamond + Mathdesign = OK (but without textsc)
  60. %usepackage[utopia]{mathdesign} % font: Utopia + MathDesign math = OK (but without textsc)
  61. %usepackage{bookman} % font: Bookman + default math = OK (but math doesn't really fit)
  62. %usepackage{concrete} % font: Concrete + Euler VM = OK (a little weird but nice math)
  63. %usepackage{mathpazo} % font: Palatino + Palatino Math = OK (very nice)
  64. % large math symbols with some fonts (package: exscale): e.g. mathmazo
  65. usepackage{exscale}
  66.  
  67. % line numbers (package: lineno)
  68. %usepackage[switch,pagewise]{lineno}
  69. %linenumbers % turn on line numbering
  70.  
  71. % quotes above chapters (package: epigraph)
  72. usepackage{epigraph}
  73. setlength{epigraphrule}{0.0pt} % width of the epigraph rule
  74. renewcommand{epigraphsize}{footnotesize} % set epigraph font
  75.  
  76. % line spacing (package: setspace)
  77. usepackage{setspace}
  78. %newcommand{defaultspace}{1.28} % default space (35 line per page) for default font, mathpazo font
  79. newcommand{defaultspace}{1.1}
  80. setstretch{defaultspace} % redefine spacing between lines (so there are 35 lines per page)
  81.  
  82. % put "." behind chapter section numbers
  83. %renewcommand thechapter{arabic{chapter}.}
  84. %renewcommand thesection{arabic{section}.}
  85. %renewcommand thesubsection{arabic{section}.arabic{subsection}.}
  86. %renewcommand thesubsubsection{arabic{section}.arabic{subsection}.arabic{subsubsection}.}
  87.  
  88. %fancy chapters (package: fncychap)
  89. %usepackage[Sonny_mod]{./styles/fncychap_mod}
  90. usepackage[Sonny]{fncychap}
  91. ChRuleWidth{1.0pt}
  92. ChNameVar{rmLARGEflushleft}
  93. ChNumVar{rmhuge}
  94. ChTitleVar{rmbfseriesHugeflushleft}
  95.  
  96. % fancy headers and footers (package: fancyhdr)
  97. usepackage{fancyhdr}
  98. pagestyle{fancy}
  99. % running title as ''1 - Title'', plus font as footnotesize
  100. renewcommand{chaptermark}[1]{markboth{footnotesizethechapter{,-,}#1}{}}
  101. % running title as ''Chapter 1. Title'', plus font as footnotesize
  102. %renewcommand{chaptermark}[1]{markboth{footnotesize chaptername thechapter {~-~} #1}{}}
  103. fancyhf{}
  104. fancyhead[LE,RO]{footnotesize thepage}
  105. fancyhead[RE,LO]{footnotesize nouppercase{leftmark}}
  106. renewcommand{headrulewidth}{0.4 pt}
  107. renewcommand{footrulewidth}{0.0 pt}
  108. % creating empty pages: no headers on empty pages before new chapter
  109. makeatletter
  110. renewcommand{cleardoublepage}{clearpageif@twoside ifoddc@pageelse
  111. thispagestyle{empty}
  112. hbox{}newpageif@twocolumnhbox{}newpagefififi}
  113. makeatother
  114.  
  115. % hyperlinks (package: hyperref)
  116. usepackage[plainpages=false,unicode=true,hyperfootnotes,hyperindex,pagebackref,backref=page]{hyperref}
  117. % define pdf document properties
  118. hypersetup{
  119. %colorlinks=true, %set 'true' for web version
  120. colorlinks=false,pdfborder=0, %set 'false' for print version
  121. linkcolor=red,anchorcolor=red,citecolor=blue,filecolor=cyan,
  122. pagecolor=green,urlcolor=red,
  123. %bookmarksopen=false,bookmarksnumbered=false,
  124. %pdfpagemode=FullScreen,
  125. %pdfpagemode=UseOutlines,
  126. pdftitle={Error estimation in quantitative image analysis},
  127. pdfauthor={Hennadii Madan},
  128. pdfsubject={PhD thesis (University of Ljubljana, Faculty of Electrical Engineering, Slovenia)},
  129. pdfkeywords={medical image analysis, medical image processing, bayeasian, statisitcs},
  130. baseurl={http://lit.fe.uni-lj.si},
  131. pdfview={Fit},
  132. pdfstartpage={1},
  133. pdfstartview={Fit}
  134. %??keywords
  135. }
  136. % back reference citations ("cited on page X")
  137. renewcommand*{backref}[1]{}
  138. renewcommand*{backrefalt}[4]{
  139. ifcase #1
  140. (not cited)
  141. or
  142. (cited on page~#2)
  143. else
  144. (cited on pages~#2)
  145. fi}
  146. renewcommand*{backrefsep}{, }
  147. renewcommand*{backreftwosep}{ and~}
  148. renewcommand*{backreflastsep}{ and~}
  149.  
  150. % footnotes (packages: fnpos, dblfnote, fnbreak)
  151. usepackage{fnpos}
  152. makeFNbottom % footnotes at the bottom of the page
  153. makeFNbelow % footnotes places below the last floats on the page
  154. usepackage{dblfnote}
  155. DFNcolumnsep 1.5columnsep % set the distance between footnote columns
  156. %DFNtrysingle % try to set footnotes in one column
  157. DFNalwaysdouble % always set footnotes in two columns
  158. makeatletter % set space between text and footnote (1em = one line)
  159. renewcommandfootnoterule{
  160. vspace{1.5em}
  161. kern-3p@hrule@width.4columnwidth
  162. kern2.6p@}
  163. makeatother
  164. %interfootnotelinepenalty=10000 % prevent footnotes to be placed on two pages or columns
  165. interfootnotelinepenalty=5000 % footnotes most likely will not be placed on two pages or columns
  166. % define the unnumbered footnote command (use symbolfootnote[0]{footnote})
  167. longdefsymbolfootnote[#1]#2{begingroupdefthefootnote{fnsymbol{footnote}}footnote[#1]{#2}endgroup}
  168. % displays warning if footnotes are split across pages
  169. usepackage{fnbreak}
  170.  
  171. % add stared chapters to toc (package: tocbibind): bibliography and index
  172. usepackage[chapter,nottoc,notlot,notlof]{tocbibind}
  173.  
  174. % table of contents (package: tocloft), option 'titles' for typesetting titles like in 'fncychap'
  175. usepackage[titles,subfigure]{tocloft}
  176. renewcommand{cftchapleader}{bfseriescftdotfill{cftsubsecdotsep}} % bold dots follow chapteras in subsection
  177. renewcommand{cftsecleader}{bfseriescftdotfill{cftsubsecdotsep}} % bold dots follow section as in subsection
  178. %setlength{cftaftertoctitleskip}{1.0cm} % space after toc title
  179. renewcommand{cftchapfont}{largebfseries} % change chapter title font
  180. setlength{cftbeforechapskip}{0.5cm} % space between chapters
  181. setlength{cftbeforesecskip}{0.25cm} % space between sections
  182. setlength{cftbeforesubsecskip}{0.05cm} % space between subsections
  183.  
  184. % index (package: makeidx)
  185. %usepackage{makeidx}
  186. %makeindex
  187. % text in multiple columns (package: multicol): to print such index
  188. usepackage{multicol}
  189. % format index (package: doc): set index chapter and add it to toc [modified style to set index epigraph]
  190. %usepackage{./styles/doc_mod}
  191. %IndexPrologue{chapter*{Index}markboth{Index}{Index}addcontentsline{toc}{chapter}{protect{Index}}}
  192.  
  193. % abbreviations {package: acronym}
  194. usepackage[printonlyused]{acronym}
  195.  
  196. % glossary (package: glossary) [modified style in order to modify the glossary header]
  197. %usepackage[style=altlist,acronym=true,section=false,number=page,toc=true,hyper=true,cols=2]{./styles/glossary_mod}
  198. % order to make the glossary
  199. %makeglossary
  200. % order to make the acronyms
  201. %makeacronym
  202. %!! glossary package does not work with acronym package, but do not need them anyway cos I have footnotes
  203.  
  204. % wrap text around floats (package: floatflt)
  205. usepackage{floatflt}
  206.  
  207. % break tabular across pages (package: supertabular)
  208. usepackage{supertabular}
  209.  
  210. % float captions (package: caption)
  211. usepackage[labelsep=period, labelfont={small,bf}, textfont=small,
  212. tableposition=below,
  213. % aboveskip=-0.3cm, % no idea why Tomaz had it, it causes
  214. %captions to overlap the graphical data
  215. belowskip=0.5cm, width=0.9textwidth]{caption}
  216. renewcommand{thefigure}{thechapter.arabic{figure}}
  217. renewcommand{thetable}{thechapter.arabic{table}}
  218. renewcommand{theequation}{thechapter.arabic{equation}}
  219. %% THIS NO LONGER WORKS! BECAUSE https://tex.stackexchange.com/a/139509/88195
  220. % subfigures (package: subfigure) [modified, so counters are not re-defined]
  221. % usepackage[loose]{./styles/subfigure_mod}
  222. %% SUBCAPTION (E.G.) IS TO BE USED INSTEAD (see HENNADII!!! comment below)
  223.  
  224. % bibliography (package: natbib) [modified style in order to include epigraph in bibliography]
  225. usepackage[round,comma,sort&compress,nonamebreak]{./styles/natbib_mod}
  226. setlength{bibsep}{0.25cm} % set the bibliography line spacing
  227.  
  228. % landscape oriented pages (package: lscape)
  229. usepackage{lscape}
  230.  
  231. % date and time formatting (package: datetime)
  232. usepackage{datetime}
  233. %newcommand{reviewtime}{vspace{-0.5cm} large textit{~\~\DRAFT VERSION:~{today}~@~{currenttime}\}} % 'DRAFT VERSION: date @ time'
  234. newcommand{reviewtime}{Ljubljana, 2018}
  235.  
  236. % dropped captials (package: lettrine)
  237. usepackage{lettrine}
  238. setcounter{DefaultLines}{2}
  239. %renewcommand{DefaultLoversize}{0.8}
  240. %renewcommand{LettrineTextFont}{scshape}
  241.  
  242. % floating figures and wrapped text around them (package: floatflt)
  243. usepackage{floatflt}
  244. usepackage{color,soul}
  245. usepackage{booktabs}
  246. usepackage{makecell}
  247. usepackage{cleveref}
  248.  
  249.  
  250.  
  251. % USER-DEFINED COMMANDS
  252. % single reference, parenthesis version
  253. newcommand{srefp}[2]
  254. {ifthenelse{equal{#1}{figure} OR equal{#1}{table} OR equal{#1}{equation}}
  255. {(#1~ref{#2}, p.~pageref{#2})}
  256. {(#1~ref{#2}, str.~pageref{#2})}}
  257. % single reference, text version
  258. newcommand{sreft}[2]
  259. {ifthenelse{equal{#1}{figure} OR equal{#1}{table} OR equal{#1}{equation} OR equal{#1}{Figure} OR
  260. equal{#1}{Table} OR equal{#1}{Equation}}
  261. {#1~ref{#2} (p.~pageref{#2})}
  262. {#1~ref{#2} (str.~pageref{#2})}}
  263. % double reference, parenthesis version
  264. newcommand{drefp}[3]
  265. {ifthenelse{equal{#1}{figures} OR equal{#1}{tables} OR equal{#1}{equations}}
  266. {(#1~ref{#2}, p.~pageref{#2} and~ref{#3}, p.~pageref{#3})}
  267. {(#1~ref{#2}, str.~pageref{#2} in~ref{#3}, str.~pageref{#3})}}
  268. % double reference, text version
  269. newcommand{dreft}[3]
  270. {ifthenelse{equal{#1}{figures} OR equal{#1}{tables} OR equal{#1}{equations} OR equal{#1}{Figures} OR
  271. equal{#1}{Tables} OR equal{#1}{Equations}}
  272. {#1~ref{#2} (p.~pageref{#2}) and~ref{#3} (p.~pageref{#3})}
  273. {#1~ref{#2} (str.~pageref{#2}) in~ref{#3} (str.~pageref{#3})}}
  274.  
  275. % the caption in the 2nd language
  276. newcommand{othercaption}[2]
  277. {ifthenelse{equal{#1}{figure}}
  278. {addtocounter{figure}{1}ContinuedFloatparbox[c]{0.9textwidth}{small textbf{Slika thefigure.}~#2}}
  279. {addtocounter{table}{1}ContinuedFloatparbox[c]{0.9textwidth}{small textbf{Tabela thetable.}~#2}}}
  280.  
  281. % paragraph with the dropped capital (lettrine)
  282. newcommand{parlet}[3]
  283. %{fontfamily{ptm} lettrine{#1}{#2} #3 fontfamily{cmr}}
  284. {lettrine{#1}{#2} #3}
  285.  
  286. % define table rules (normal and big)
  287. newcommand{tablerule}{rule{0pt}{2ex}}
  288. newcommand{Tablerule}{rule{0pt}{3ex}}
  289. %-------------------------
  290. %%>>>>>>>>>>>>>>> HENNADII!!! <<<<<<<<<<<<<<<
  291. usepackage{amsthm}
  292. newtheorem{theorem}{Theorem}
  293. usepackage{xspace}
  294. usepackage{siunitx}
  295. usepackage{mathtools}
  296. usepackage{gensymb}
  297. usepackage{bm}
  298.  
  299.  
  300. usepackage{subcaption} %for a,b,c,d in figures
  301. captionsetup{subrefformat=parens}
  302.  
  303. % MAKE MATLAB/MPL2TIKZ WORK:
  304. %% MATLAB 2 TIKZ PREAMBLE
  305. usepackage{tikz}
  306. % usetikzlibrary{external}
  307. % tikzset{external/system call={pdflatex tikzexternalcheckshellescape
  308. % -halt-on-error
  309. % -interaction=batchmode
  310. % -jobname "image" "texsource"
  311. % && pdftops -eps "image.pdf"}}
  312. % tikzexternalize[shell escape=-enable-write18]
  313. usepackage{pgfplots}
  314. pgfplotsset{compat=newest}
  315. %% the following commands are sometimes needed
  316. usetikzlibrary{plotmarks}
  317. usepackage{grffile}
  318. %% you may also want the following commands
  319. %pgfplotsset{plot coordinates/math parser=false}
  320. newlengthfigureheight
  321. newlengthfigurewidth
  322.  
  323. %% ACRONYMS
  324. usepackage[acronym]{glossaries}
  325. % makeglossaries
  326.  
  327. %>>>>>>>>>>>>>>> FOR CHAPTER 2 (AUTO_GS_ARTICLE)
  328. newacronym{32R}{32R}{3D/2D image registration}
  329. newacronym{23R}{32R}{3D/2D image registration}
  330. newacronym{R32R}{R32R}{rigid 3D/2D image registration}
  331. % Despite Franjo's notes 23R is used somewhat more frequently used than 32R
  332. newacronym{IB23R}{IB23R}{image-based 3D/2D image registration}
  333. newacronym{IB32R}{IB32R}{image-based 3D/2D image registration}
  334. % newacronym{RWT}{RWT}{regression without truth}
  335. newacronym{SR}{SR}{success rate}
  336. newacronym{TRE}{TRE}{target registration error}
  337. newacronym{mTRE}{mTRE}{mean target registration error}
  338. newacronym{FRE}{FRE}{fiducial registration error}
  339. newacronym{FLE}{FLE}{fiducial localization error}
  340. newacronym{mPD}{mPD}{mean projection distance}
  341. newacronym{OR}{OR}{operating room}
  342. newacronym{IGI}{IGI}{image-guided interventions}
  343. newacronym{IGRT}{IGRT}{image-guided radiation therapy}
  344. newacronym{SM}{SM}{similarity measure}
  345. newacronym{GSC}{GSC}{gold standard creation}
  346. newacronym{DM}{DM}{detected markers}
  347. newacronym{PM}{PM}{detected markers}
  348. newacronym{AVM}{AVM}{arteriovenous malformation}
  349. newacronym{3D-DSA}{3D-DSA}{3D digital subtraction angiogram}
  350. newacronym{DSA}{DSA}{digital subtraction angiogram}
  351. newacronym{2D-DSA}{2D-DSA}{2D digital subtraction angiogram}
  352. newacronym{XA}{XA}{X-ray angiography}
  353. newacronym{CBCT}{CBCT}{cone-beam computed tomogram}
  354. newacronym{CT}{CT}{computed tomography}
  355. newacronym{MR}{MR}{magnetic resonance}
  356. newacronym{3D}{3D}{three-dimensional}
  357. newacronym{2D}{2D}{two-dimensional}
  358. newacronym{DRR}{DRR}{digitally reconstructed radiograph}
  359. newacronym{AHC}{AHC}{agglomerative hierarchical clustering}
  360. newacronym[firstplural=regions of interest (ROIs)]{ROI}{ROI}{region of interest}
  361. newacronym[firstplural=volumes of interest (VOIs)]{VOI}{VOI}{volume of interest}
  362. newacronym{rms}{rms}{root mean squared}
  363. newacronym{SVD}{SVD}{singular value decomposition}
  364. newacronym{WHO}{WHO}{World Health Organization}
  365. newacronym{dof}{DoF}{degrees of freedom}
  366. newacronym{SOD}{SOD}{source to object distance}
  367. newacronym{SID}{SID}{source to detector distance}
  368. newacronym{PA}{PA}{primary angle}
  369. newacronym{SA}{SA}{secondary angle}
  370. newacronym{WP}{WP}{working projection}
  371. newacronym{OP}{OP}{orthogonal to the working projection}
  372.  
  373. %>>>>>>>>>>>>>>> FOR CHAPTER 3 (ARTICLE_REFFREE_REGRESSION)
  374. newacronym{rmse}{RMSE}{root mean square error}
  375. newacronym{mcmc}{MCMC}{Markov chain Monte-Carlo}
  376. newacronym{ef}{EF}{left-ventricular ejection fraction}
  377. newacronym{qib}{QIB}{quantitative imaging biomarker}
  378. newacronym{qiba}{QIBA}{quantitative imaging biomarker alliance}
  379. newacronym{mle}{MLE}{maximum likelihood estimate}
  380. newacronym{map}{MAP}{maximum a posteriori}
  381. newacronym{mri}{MRI}{magnetic resonance image}
  382. newacronym{ms}{MS}{multiple sclerosis}
  383. newacronym{tll}{TLL}{total lesion load}
  384. newacronym{ct}{CT}{computed tomography}
  385. newacronym{cns}{CNS}{central neural system}
  386. newacronym{ls}{LS}{least squares}
  387. newacronym{mvg}{MVG}{multivariate Gaussian}
  388. newacronym{umcl}{UMCL}{University Medical Centre Ljubljana}
  389. newacronym{iprg}{IPRG}{Interdisciplinary Pharmacogenomics Review Group}
  390. % newacronym{cod}{COD}{coefficient of determination}
  391.  
  392.  
  393. %>>>>>>>>>>>>>>> FOR CHAPTER 4 (PRACTICAL PRIORS)
  394. newacronym{csf}{CSF}{cerebrospinal fluid}
  395. newacronym{cr}{CR}{credible region}
  396. newacronym{ci}{CI}{credible interval}
  397. newacronym{nuts}{NUTS}{No U-Turn Sampler}
  398. newacronym{rwt}{RWT}{regression without truth}
  399. newacronym{lkj}{LKJ}{Lewandowski Kurowicka Joe}
  400. newacronym{std}{STD}{standard deviation}
  401. % newacronym{rmse}{RMSE}{root mean square error}
  402. % newacronym{mcmc}{MCMC}{Markov chain Monte-Carlo}
  403. % newacronym{ef}{EF}{left-ventricular ejection fraction}
  404. % newacronym{qib}{QIB}{quantitative imaging biomarker}
  405. % newacronym{qiba}{QIBA}{quantitative imaging biomarker alliance}
  406. % newacronym{mle}{MLE}{maximum likelihood estimate}
  407. % newacronym{map}{MAP}{maximum a posteriori}
  408. % newacronym{mri}{MRI}{magnetic resonance image}
  409. newacronym{mr}{MR}{magnetic resonance}
  410. % newacronym{ms}{MS}{multiple sclerosis}
  411. % newacronym{tll}{TLL}{total lesion load}
  412. % newacronym{ct}{CT}{computed tomography}
  413. % newacronym{cns}{CNS}{central neural system}
  414. % newacronym{ls}{LS}{least squares}
  415. % newacronym{mvg}{MVG}{multivariate Gaussian}
  416. % newacronym{umcl}{UMCL}{University Medical Centre Ljubljana}
  417. newacronym{umcm}{UMCM}{University Medical Centre Maribor}
  418. % newacronym{iprg}{IPRG}{Interdisciplinary Pharmacogenomics Review Group}
  419. % newacronym{cod}{COD}{coefficient of determination}
  420. newacronym{mm}{MM}{measurement method}
  421. newcommand{mm}{glspl{mm}}
  422. newacronym{gs}{GS}{gold standard}
  423. newcommand{gs}{gls{gs}}
  424. newacronym{wm}{WM}{white matter}
  425. newacronym{gm}{GM}{grey matter}
  426. newacronym{mae}{MAE}{mean absolute error}
  427.  
  428.  
  429.  
  430. %% END ACRONYMS
  431. %% MY WHIMS
  432. newcommand{noun}[1]{textit{#1}}% Original formatting of nouns
  433. DeclareMathOperator*{argmin}{arg!min}
  434. DeclareMathOperator*{argmax}{arg!max}
  435. % shortcuts to save typing
  436. % newcommand{gs}{gold standardxspace}
  437. newcommand{Gs}{Gold standardxspace}
  438. newcommand{IGI}{gls{IGI} }
  439. newcommand{IGRT}{gls{IGRT} }
  440. %%>>>>>>>>>>>>>>> END HENNADII!!! <<<<<<<<<<<<<<<
  441.  
  442. %--------------------------
  443. % BEGIN DOCUMENT
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