# I am losing my indentations after the figure's caption

I am writing my M.Sc. thesis (biochemistry). According to the Graduate Office, full-page figures require that their description be on a different page. Here is my main.tex file (sample) with the picture. You will notice that I lose the indentation after the description. I was wondering how to correct that. Thank you very much for your time!!

\documentclass[12pt, oneside]{book}
\usepackage{graphicx}
\usepackage[a4paper,margin=1in]{geometry}
\usepackage{pdflscape}
\usepackage{caption}
\usepackage{csquotes}
\captionsetup[figure]{labelfont=bf}
\graphicspath{{./Chapters/Figures/}}
\usepackage[table]{xcolor}

\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}

\usepackage{amsmath}

\usepackage{fancyhdr}
\pagestyle{fancy}
%Allows first indent and loads setspace package to be used in different documents.
\usepackage{indentfirst}
\usepackage{setspace}
\usepackage{url}

%Make cell space and scientific notation
\usepackage{longtable, cellspace, booktabs}
\setlength\cellspacetoplimit{4pt}
\setlength\cellspacebottomlimit{4pt}
\usepackage[table]{xcolor}
\usepackage{siunitx}
\sisetup{scientific-notation = true}

%Enables paragraph spacing. Saves the old indent value and restores it after loading the parskip package. Otherwise, you lose the indents.
\edef\restoreparindent{\parindent=\the\parindent\relax}
\usepackage{parskip}
\restoreparindent

\usepackage[backend=biber,style=numeric,,sorting=none]{biblatex}

\usepackage{cleveref}

\begin{document}

Another limitation of Nordling’s model is that it assumes a constant likelihood for each event, which is not always true.
For example, breast cancer follows the sixth power until the menopause and then deviates inwards suggesting that later events are less likely to occur after menopause.
This makes sense since breast cancer has hormonal risk factors.
Increased exposure to estrogen increases the risk of breast cancer.
Thus, factors that increase the number of menstrual cycles, such as early menarche, nulliparity, and late onset of menopause, also increase the risk of breast cancer.

Similarly, reducing the number of menstrual cycles through a longer lactation period seems to be protective.
\begin{figure}[htbp]
\includegraphics[width=\textwidth]{Figure3.png}
\label{fig:mortality}
\end{figure}
\clearpage
\null\vspace{\fill}
\captionof{figure}[Log-log plots of cancer mortality rates in Canada for 2010]{\textbf{Log-log plots of cancer mortality rates in Canada for 2010.} This figures shows that cancer overall requires at least six steps for both men and women (A,B). Additionally, the mathematical modelling of the influence of estrogen levels on breast cancer is consistent with the epidemiological data (C). Colon cancer in women is used as control because it is hormonally independent (D). \textit{Data: CANSIM tables 051-0522 and 102-0522, Statistics Canada. Accessed: April 4th, 2015.}}
\vspace{\fill}
\clearpage

Nordling’s equation can be modified so the likelihood of an independent event changes as a function of the time of exposure to a factor (e.g. carcinogen, hormone), and the order of the cellular change which it affects. Mathematically, the probability of an event is proportional to:
$$t_{0}^{s-1}(t-t_{0})^{r-s-1}$$
where to is the age of initial exposure, t is the age at diagnosis, r is the number of steps for carcinogenesis, and s is the order of the event (i.e. first, second,…,r\textsuperscript{th}).

\end{document}


• Place your \captionof inside a group the problem disappears { \captionof{figure}[]{...} }. – Salim Bou Aug 26 '15 at 17:48

The problem with your code is that you are using \captionof without a protecting box or environment and this, as you experienced, gives bad results. This is mentioned on page 18 of the caption documentation:

...so you should use both \captionof and \captionof* only inside boxes or environments,...

You can add some enclosing environment, a minipage, for example:

\documentclass[12pt, oneside]{book}
\usepackage{graphicx}
\usepackage[a4paper,margin=1in]{geometry}
\usepackage{pdflscape}
\usepackage{caption}
\usepackage{csquotes}
\captionsetup[figure]{labelfont=bf}
\graphicspath{{./Chapters/Figures/}}
\usepackage[table]{xcolor}

\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}

\usepackage{amsmath}

\usepackage{fancyhdr}
\pagestyle{fancy}
%Allows first indent and loads setspace package to be used in different documents.
\usepackage{indentfirst}
\usepackage{setspace}
\usepackage{url}

%Make cell space and scientific notation
\usepackage{longtable, cellspace, booktabs}
\setlength\cellspacetoplimit{4pt}
\setlength\cellspacebottomlimit{4pt}
\usepackage[table]{xcolor}
\usepackage{siunitx}
\sisetup{scientific-notation = true}

%Enables paragraph spacing. Saves the old indent value and restores it after loading the parskip package. Otherwise, you lose the indents.
\edef\restoreparindent{\parindent=\the\parindent\relax}
\usepackage{parskip}
\restoreparindent

\usepackage[backend=biber,style=numeric,,sorting=none]{biblatex}

\usepackage{cleveref}

\begin{document}

Another limitation of Nordling’s model is that it assumes a constant likelihood for each event, which is not always true.
For example, breast cancer follows the sixth power until the menopause and then deviates inwards suggesting that later events are less likely to occur after menopause.
This makes sense since breast cancer has hormonal risk factors.
Increased exposure to estrogen increases the risk of breast cancer.
Thus, factors that increase the number of menstrual cycles, such as early menarche, nulliparity, and late onset of menopause, also increase the risk of breast cancer.

Similarly, reducing the number of menstrual cycles through a longer lactation period seems to be protective.
\begin{figure}[htbp]
\includegraphics[width=\textwidth]{example-image-a}
\label{fig:mortality}
\end{figure}
\clearpage
\null\vspace{\fill}
\noindent
\begin{minipage}{\textwidth}
\captionof{figure}[Log-log plots of cancer mortality rates in Canada for 2010]{\textbf{Log-log plots of cancer mortality rates in Canada for 2010.} This figures shows that cancer overall requires at least six steps for both men and women (A,B). Additionally, the mathematical modelling of the influence of estrogen levels on breast cancer is consistent with the epidemiological data (C). Colon cancer in women is used as control because it is hormonally independent (D). \textit{Data: CANSIM tables 051-0522 and 102-0522, Statistics Canada. Accessed: April 4th, 2015.}}
\end{minipage}
\vspace{\fill}
\clearpage

Nordling’s equation can be modified so the likelihood of an independent event changes as a function of the time of exposure to a factor (e.g. carcinogen, hormone), and the order of the cellular change which it affects. Mathematically, the probability of an event is proportional to:
$$t_{0}^{s-1}(t-t_{0})^{r-s-1}$$
where to is the age of initial exposure, t is the age at diagnosis, r is the number of steps for carcinogenesis, and s is the order of the event (i.e. first, second,…,r\textsuperscript{th}).

\end{document}


The result:

I'd like to suggest you, however, the fltpage package and its FPfigure environment to easily typeset captions in a different page. A complete example:

\documentclass[12pt, oneside]{book}
\usepackage{graphicx}
\usepackage[a4paper,margin=1in]{geometry}
\usepackage{caption}
\captionsetup[figure]{labelfont=bf}

\usepackage[CaptionAfterwards]{fltpage}

\usepackage{indentfirst}

%Enables paragraph spacing. Saves the old indent value and restores it after loading the parskip package. Otherwise, you lose the indents.
\edef\restoreparindent{\parindent=\the\parindent\relax}
\usepackage{parskip}
\restoreparindent

\begin{document}

Another limitation of Nordling’s model is that it assumes a constant likelihood for each event, which is not always true.
For example, breast cancer follows the sixth power until the menopause and then deviates inwards suggesting that later events are less likely to occur after menopause.
This makes sense since breast cancer has hormonal risk factors.
Increased exposure to estrogen increases the risk of breast cancer.
Thus, factors that increase the number of menstrual cycles, such as early menarche, nulliparity, and late onset of menopause, also increase the risk of breast cancer.

Similarly, reducing the number of menstrual cycles through a longer lactation period seems to be protective.

\begin{FPfigure}
\includegraphics[width=\textwidth]{example-image-a}
\label{fig:mortality}
\caption[Log-log plots of cancer mortality rates in Canada for 2010]{\textbf{Log-log plots of cancer mortality rates in Canada for 2010.} This figures shows that cancer overall requires at least six steps for both men and women (A,B). Additionally, the mathematical modelling of the influence of estrogen levels on breast cancer is consistent with the epidemiological data (C). Colon cancer in women is used as control because it is hormonally independent (D). \textit{Data: CANSIM tables 051-0522 and 102-0522, Statistics Canada. Accessed: April 4th, 2015.}}
\end{FPfigure}

\clearpage% just for the example

Nordling’s equation can be modified so the likelihood of an independent event changes as a function of the time of exposure to a factor (e.g. carcinogen, hormone), and the order of the cellular change which it affects. Mathematically, the probability of an event is proportional to:
$$t_{0}^{s-1}(t-t_{0})^{r-s-1}$$
where to is the age of initial exposure, t is the age at diagnosis, r is the number of steps for carcinogenesis, and s is the order of the event (i.e. first, second,…,r\textsuperscript{th}).

\end{document}


The result:

## Remark

Having additional vertical separation between paragraphs as well as indentation of the first lines is completely redundant and really ugly; however, I'm aware that this seems to be a University requirement and we all know that universities are not precisely well known for their typographical good taste when it comes to theses.