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brainlife / app-acpcART

This app uses the Automatic Registration Toolbox (ART) to perform ACPC alignment of the T1 image. See https://www.nitrc.org/projects/art/ for more information.
MIT License
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crop option not cropping image tightly #1

Open soichih opened 6 years ago

soichih commented 6 years ago

I have an input image that looks like this.

screenshot from 2018-03-19 14-30-37

If I pass it through ACPC alignment app, it crops nicely on X and Z axis but leaves good chunk of empty space for Y axis.

screenshot from 2018-03-19 14-32-03

I believe this causes Freesurfer to fail with following error message.

****************************************
ERROR! FOV=318.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.
****************************************

Is there something we can do to make the image crop more of the white space on Y?

kitchell commented 6 years ago

I think robustfov (which is what we are using for crop) only focuses on the z direction:

Reduce FOV of image to remove lower head and neck.

Usage: robustfov [options] -i -r robustfov [options] -i

Compulsory arguments (You MUST set one or more of): -i input filename

Optional arguments (You may optionally specify one or more of): -b size of brain in z-dimension (default 170mm) -m matrix output name (roi to full fov) -r ROI volume output name --debug turn on debugging output -v,--verbose switch on diagnostic messages -h,--help display this message

We could look into other cropping options