Investigate cutneck, find script

CoBrALab / minc-bpipe-library

Library of bpipe implemented commands commonly applied to minc datafiles, suitable for importing into other pipelines

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Investigate cutneck, find script #2

Closed raihaan closed 9 years ago

raihaan commented 9 years ago

Find cutneck script and confirm usage

gdevenyi commented 9 years ago

Any updates on cutneck?

raihaan commented 9 years ago

Yes, located. will point it your way tmrw.

On Mon, Nov 10, 2014 at 10:21 PM, Gabriel A. Devenyi < notifications@github.com> wrote:

Any updates on cutneck?

— Reply to this email directly or view it on GitHub https://github.com/CobraLab/bpipe-library/issues/2#issuecomment-62496412 .

raihaan commented 9 years ago

/home/cic/patrai/cutneck

in the scripts folder you will see 3 variations of cutneck_ANTS

_original is from CAMH _cobra is same functionality as _original, but with paths edited for use at Douglas _nonuc runs just the cutneck operation (_original and _cobra run cutneck plus nucorrect)

_cobra and _nonuc are setup to run on compute server at Douglas

gdevenyi commented 9 years ago

Cutneck applies the following transformations

linearly register subject to template
apply inverse transformation to template_headmask to produce subject_headmask
autocrop -bbox subject_headmask.mnc -isoexpand 5 subject.mnc subject_cropped.mnc

gdevenyi commented 9 years ago

Implemented.