in #10117 mail (see below) for coregistering target to MNI_152 using flirt,
should "-init flirtaffinetransf.mat" for replacing line 69 be a typo of
"-omat flirtaffinetransf.mat" ?
i.e.
$FSLDIR/bin/flirt -in target.hdr -ref $M -out
target_to_MNI152.hdr -omat flirtaffinetransf.mat
-applyxfm
but not
$FSLDIR/bin/flirt -in target.hdr -ref $M -out
target_to_MNI152.hdr -init flirtaffinetransf.mat
-applyxfm
Thanks.
#10117
unfortunately, there is no easy way (so far) to
convert an areg .dof into a flirt .mat... So the best
way to continue the tbss preprocessings is to register
your diffusion images in two steps.
You can do so by editing tbss_3_postreg script and by:
1) replacing the areg transformation from the best
target to the MNI152 by the flirt one in the
tbss_3_postreg script:
- erase line 68
- replace line 69: ${D}/transformation target.hdr
target_to_MNI152.hdr -dofin target_to_MNI152.dof
-linear -target $M
by -> $FSLDIR/bin/flirt -in target.hdr -ref $M -out
target_to_MNI152.hdr -init flirtaffinetransf.mat
-applyxfm
2) separating the two transformations applied to your
diffusion images:
- replace line 76: ${D}/transformation2 ${f}.hdr
${f}_to_${best}_nonlinear_hr.hdr -dofin2
${f}_to_${best}_nonlinear.dof -dofin1
../stats/target_to_MNI152.dof -linear -target
../stats/$M
by -> ${D}/transformation ${f}.hdr
${f}_to_${best}_tmp.hdr -dofin
${f}_to_${best}_nonlinear.dof -linear -target
${best}.hdr
followed by -> $FSLDIR/bin/flirt -in
${f}_to_${best}_tmp.hdr -ref $M -out
${f}_to_${best}_nonlinear_hr.hdr -init
flirtaffinetransf.mat -applyxfm
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