External Email - Use Caution

Hi all,

This is a reproduction of GitHub issue 1010. There is a section of recon-all (L5927-5930 in current dev) that states:

# MOD: turn on T2/FLAIR pial editing when FLAIR specified # This can backfire, eg, if not all the preceeding steps # are included set DoT2pial = 1;

This seems an intentional decision to make -T2 activate -T2pial (and similar for -FLAIR), which I suppose is a response to people running `recon-all -i $T1 -T2 $T2 -all` without `-T2pial`. However, it also activates with -autorecon1 and -autorecon2, which will not run -pial before -T2pial. Would you all consider this a bug or a caveat emptor kind of situation?

Would it make sense to add the following to -autorecon1 and -autorecon2 (hopefully this formats okay)?

diff --git a/scripts/recon-all b/scripts/recon-all index 4b98118264..0655097ab9 100755 --- a/scripts/recon-all +++ b/scripts/recon-all @@ -6869,6 +6869,7 @@ while( $#argv != 0 ) breaksw

case "-autorecon1": + set DoT2pial = 0; set DoCreateBaseInput = 1; set DoMotionCor = 1; set DoTalairach = 1; @@ -6911,6 +6912,7 @@ while( $#argv != 0 ) set DoRemoveNeck = 0; set DoSkullLTA = 0; set DoSegStats = 0; + set DoT2pial = 0; set DoCANormalize = 1; set DoGCAReg = 1; set DoCALabel = 1;

In any case, I am now adding -noT2pial and -noFLAIRpial to -T2 calls that aren't -all as well, which seems safe for writing commands that will work for both FreeSurfer 6 and 7.

Thanks, Chris