retitle 589352 clarify in documentation/--help the order of transformations severity 589352 wishlist thanks
ah... I guess you mean that the order of transformations in command line
is not the order of application but more inline with matrix
representation for linear transformations when new transformation is
obtained by prepending matrix product with yet another matrix...
and indeed reversing the order on this example make results consistent!
script reproduce-order2.sh, just in case...
Cool! I will check on the rest of the data ;)
So, it is kinda RTFM issue ;) But, whenever ants.pdf somewhat describes it
(e.g. Figure 7) in this reverted application order, although even more
confusing to me since I would expect BA not AB... but --help is actually
what confused us I think:
you can also string together series of mappings --- e.g.:
MyAffine.txt MySecondAffine.txt MyWarp.nii.gz MySecondWarp.nii.gz -i
MyInverseAffine.txt --- this can be an arbitrarily long series.
so, it suggests that series of transformations goes T1, T2, not T2, T1
Altogether it seems to be somewhat confusing documentation...? or
it is just me?
N.B. thus retitling and lowering severity of this report.
Thanks!
On Sun, 18 Jul 2010, brian avants wrote:
> i believe this is the key to unlock your transforms:
> trans_mni2anat=" -i anat2mni_Affine.txt anat2mni_InverseWarp.nii.gz "
> trans_anat2func="-i raiders_func2anat_Affine.txt"
> trans_mni2func=" $trans_anat2func $trans_mni2anat "
> switch both aff/inv and the trans order ....
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