Thanks!
Well, the thing is that gcc is a requirement for fftw, see here:
glerma@axial:/Users/glerma/soft/mrtrix3:(master)$
# brew uninstall fftw
Uninstalling /usr/local/Cellar/fftw/3.3.8... (52 files, 10.9MB)
glerma@axial:/Users/glerma/soft/mrtrix3:(master)$
# brew uninstall gcc
Uninstalling /usr/local/Cellar/gcc/8.2.0... (1,413 files, 295.9MB)
glerma@axial:/Users/glerma/soft/mrtrix3:(master)$
# brew install fftw
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 1 tap (homebrew/core).
==> New Formulae
ahoy opencv@3
==> Updated Formulae
ansible carla embulk fonttools libgpg-error mpd pulumi swiftlint vips zabbix
audacious checkbashisms fauna-shell gearman mongodb mpv scummvm typescript wtf zeromq
bower dosbox-x fluid-synth imagemagick mongodb@3.6 open-babel sphinx urbit yara
==> Deleted Formulae
cputhrottle
==> Installing dependencies for fftw: gcc
==> Installing fftw dependency: gcc
==> Downloading https://homebrew.bintray.com/bottles/gcc-8.2.0.mojave.bottle.2.tar.gz
Already downloaded: /Users/glerma/Library/Caches/Homebrew/downloads/5e336edb977168e21c1c3d0e1d374b76c39a8780ccee6b1e2d81a832a3f01118--gcc-8.2.0.mojave.bottle.2.tar.gz
==> Pouring gcc-8.2.0.mojave.bottle.2.tar.gz
🍺 /usr/local/Cellar/gcc/8.2.0: 1,413 files, 295.9MB
==> Installing fftw
==> Downloading https://homebrew.bintray.com/bottles/fftw-3.3.8.mojave.bottle.tar.gz
Already downloaded: /Users/glerma/Library/Caches/Homebrew/downloads/3421e4a325c9d0baafe341cc32a1b0df238231473fde94c47f6b28256db41683--fftw-3.3.8.mojave.bottle.tar.gz
==> Pouring fftw-3.3.8.mojave.bottle.tar.gz
🍺 /usr/local/Cellar/fftw/3.3.8: 52 files, 10.9MB
The same happens if we try to install brew install mrtrix3, the same files are installed as dependencies…
I uninstalled again fftw and gcc and used ./configure again and I have the same
ERROR: unable to determine pointer size!
I tried to brew uninstall gcc and then manually installing fftw, but when I do ./configure I get a similar error regarding the pointer size.
Can you think in something I could try that does not involve reinstalling the whole operating system again? 
thanks!
Gari