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Mouse-Imaging-Centre / pydpiper

Python code for flexible pipeline control
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CSV column for MAGeT mask? #415

Open gdevenyi opened 5 years ago

gdevenyi commented 5 years ago

The derivatives.csv and analysis.csv both contain an lsq6_mask_file and nlin_mask_file column, are either of these the mask generated by maget masking? If not, can you add that.

Related, if I wanted masks for every subject, which one should I use, the nlin mask, or the maget mask?

bcdarwin commented 5 years ago

The lsq6_mask_file will be the one created by MAGeT if --(maget-)mask was enabled, and the resampled initial model mask if not.

If you want a mask in lsq6 space, use the lsq6_mask_file, and in nlin space, use the nlin_mask_file or ..._nlin/nlin-3_mask.mnc .

gdevenyi commented 5 years ago

Is there a mask available in native space? Or will I have to generate that myself?

bcdarwin commented 5 years ago

There should be native masks (used for N3 I think) but I don't think they are saved anywhere so they'll probably be in a tmp folder. Also I'm not sure if the nicer masks from MAGeT get propagated here or if the initial model mask only is used. Let me look into this, might be worth adding to CSV ...

From: Gabriel A. Devenyi notifications@github.com Sent: January 1, 2019 2:20:28 PM To: Mouse-Imaging-Centre/pydpiper Cc: Ben Darwin; Comment Subject: Re: [Mouse-Imaging-Centre/pydpiper] CSV column for MAGeT mask? (#415)

Is there a mask available in native space? Or will I have to generate that myself?

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gdevenyi commented 5 years ago

+1 for adding.

My muskrat model/atlas build is a bit iterative so I'm re-pre-processing the native scans as I get better outputs from pydpiper so I need to get stuff back in native space.