My suggestion would be to clip the image contents within LaTeX; graphicx allows for that:

\documentclass{article}
\usepackage{graphicx,subcaption}
\begin{document}
\begin{figure}
\centering
\setbox1=\hbox{\includegraphics{example-image-a}}%
\subcaptionbox{}{\centering\includegraphics[scale=0.5,viewport=.5\wd1 0 \wd1 \ht1,clip]{example-image-a}}%
\qquad
\setbox1=\hbox{\includegraphics{example-image-b}}%
\subcaptionbox{}{\centering\includegraphics[scale=0.5,viewport=0 0 .5\wd1 \ht1,clip]{example-image-b}}
\caption{This is main figure}
\end{figure}
\end{document}
I've used example-image-a and example-image-b (from mwe) above, although you will use the same image. As such, you'll only need to capture the image in box 1 once. Note how the image is split in half (at the .5\wd1 mark) with the viewport and clip combination.
Additionally, I've used subcaption, but you can manage the same with subfig.
Here is an example of breaking up a single image into six equal parts (perhaps synonymous to your situation):

\documentclass{article}
\usepackage{graphicx,subcaption}
\begin{document}
\begin{figure}
\centering
\setbox1=\hbox{\includegraphics{example-image}}%
\subcaptionbox{}{\centering\includegraphics[scale=0.5,viewport=0 0 .16667\wd1 \ht1,clip]{example-image}}%
\quad
\subcaptionbox{}{\centering\includegraphics[scale=0.5,viewport=.16667\wd1 0 .3333\wd1 \ht1,clip]{example-image}}%
\quad
\subcaptionbox{}{\centering\includegraphics[scale=0.5,viewport=.3333\wd1 0 .5\wd1 \ht1,clip]{example-image}}%
\quad
\subcaptionbox{}{\centering\includegraphics[scale=0.5,viewport=.5\wd1 0 .66667\wd1 \ht1,clip]{example-image}}%
\quad
\subcaptionbox{}{\centering\includegraphics[scale=0.5,viewport=.6667\wd1 0 .8333\wd1 \ht1,clip]{example-image}}%
\quad
\subcaptionbox{}{\centering\includegraphics[scale=0.5,viewport=.8333\wd1 0 \wd1 \ht1,clip]{example-image}}%
\caption{This is main figure}
\end{figure}
\end{document}
Each component is extracted as a sixth of the total width \wd1, one step at a time.