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CIVET Installer
http://www.bic.mni.mcgill.ca/ServicesSoftware/CIVET-2-1-0-Source-Code-Access-and-Binaries
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Add missing Helvetica font #7

Closed gdevenyi closed 4 years ago

gdevenyi commented 4 years ago

Helvetica is hard-coded in the annotation call to imagemagick during QC image generation. Sadly it also seems that those stages aren't properly catching the error code of imagemagick and so this bug went unnoticed. Found when I starting running the container on data and found all the QC images don't have any text on them.

We need to install the named font Helvetica because imagemagick doesn't honour overrides in fontconfig to use another similar font.

gdevenyi commented 4 years ago

Ref:

mogrify -stroke green -pointsize 16 -font Helvetica -annotate 0x0+10.3209102902375+9.88819261213722 t1 final image 100206_t1_final.mnc (native at  0.70 x  0.70 x  0.70 mm) (-lsq12) -annotate 0x0+10.3209102902375+226.962730870712 t1 non-linear registration to mni_icbm152_t1_tal_nlin_sym_09a -annotate 0x0+10.3209102902375+444.037269129288 classified image CSF  8.49%  GM 48.29%  WM 41.23%  SC  1.98%
 -annotate 0x0+10.3209102902375+661.111807387863 white surface ( 7.13%), gray surface ( 7.45%)
 /mnt/civet-denoise-output/100206/verify/100206_verify.png
mogrify-im6.q16: unable to read font `Helvetica' @ error/annotate.c/RenderFreetype/1367.
gdevenyi commented 4 years ago

Paging @prioux for a new docker build push. Merci!