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  • File equivalents between MICe-build-model.pl and MBM.py
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Equivalents for MBM.py version 1.10 (and older)

MBM.py is still under development. We are working on making sure that the filenames produced by MBM.py are intuitive (that's currently not yet the case). Here are the equivalents for any MBM.py version 1.10 or older (prior to October 31, 2014). Currently when you run a pipeline, no version information is written out to any of the files produced in your pipeline. Starting with the upcoming version, an MBM.py pipeline will write these two files:

MICe-build-model-pipeline-stages.txt
MICe-build-model-pipeline-command-and-version.txt  (<-- as of version 1.11)

So for now, if this file is not produced, you know you're running version 1.10 or older.

 

Kind of transformationMICe-build-model.plMBM.py
6 parameter transform (from native to lsq6)/transforms/{filename}_concat.xfm/transforms/{filename}_to_{init_model_name}_lsq6_{highest_number}.xfm *
12 parameter transform (average transform from lsq6 to lsq12)/transforms/{filename}-avg-lsq12.xfm/transforms/{filename}-avg-lsq12.xfm
final nonlinear transform (from lsq12 to final nlin)/transforms/{filename}-final-nlin.xfm/transforms/{filename}-final-nlin.xfm
from native all the way to final nlin/transforms/{filename}-from-native.xfmNA
from final nlin back to lsq12/transforms/{filename}_inv_nonlinear.xfm
/transforms/{filename}-final-nlin_inverse.xfm **

/transforms/{filename}-final-nlin_inverted.xfm
/transforms/{filename}-final-nlin_inverse.xfm **

from final nlin back to lsq6/transforms/{filename}-final-to_lsq6.xfm/transforms/{filename}-final-nlin_with_additional_inverted.xfm
from final nlin back to native/transforms/{filename}-to-native.xfmNA
the linear part of the final nonlinear transformation/transforms/{filename}_linear_part_of_nlin.xfm/transforms/{filename}-final-nlin_linear_part.xfm
all linear parts from lsq6 to final nlin (=lsq12 + linear part from nlin)/transforms/{filename}-final-lsq12.xfmNA
from lsq6 to final nlin space (lsq12 + final nlin)NA/transforms/{filename}-final-nlin_with_additional.xfm
the inverse of the non linear part (inv final nlin + linear from nlin)NA/transforms/{filename}-final-nlin_inverted_pure_nlin.xfm

 * depending on the kind of registration parameters you used, the "highest_number" could be:
0 (--lsq6-large-rotations-parameters (default)
4 (--lsq6-centre-estimation)
2 (--lsq6-simple)
** when using mincANTS for the non linear registration

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