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Mouse-Imaging-Centre / pydpiper

Python code for flexible pipeline control
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Generation of model is successful but jacobians are incomplete #439

Closed gdevenyi closed 4 years ago

gdevenyi commented 4 years ago

Seems we've run into some sort of FOV issue, where the jacobian space is wrong? image

gdevenyi commented 4 years ago

Followup, I'm moving up the chain of commands that generate the files in pydpiper.

The problem exists before the generation of:

neonates_extracted_20190925_processed/img_18sep18.13.sept2014_extracted/tmp/img_18sep18.13.sept2014_extracted_lsq6_lsq12_and_nlin__concat_inverted_linear_part_displ_smooth_fwhm0.08.mnc

i.e. it is not mincblob, or mincmath

gdevenyi commented 4 years ago

This appears to have been an issue with a broken nlin-2 file which was propogating its errors downstream by breaking various minc calls almost-but-no-quite.

Is this a job for minccomplete?

gdevenyi commented 4 years ago

Scratch that, it wasn't a broken file.

It looks like the root failure is ANTS is writing a cropped deformation field. I checked the input into the ANTS call and it is not cropped like that.

nzxwang commented 4 years ago

closing since this is an issue with ANTS and not pydpiper. If theres a way for minccomplete to save it, please re-open