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
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