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ERROR! FOV=289.000 > 256 Include the flag -cw256 with recon-all! #29

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chrisfilo opened this Issue Jul 27, 2018 · 1 comment

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chrisfilo commented Jul 27, 2018

Originally reported at https://neurostars.org/t/freesurfer-error-fov-256

For files with unusually large FOV freesurfer needs to perform cropping. Example image
image

Suggested solution: detect if FOV is larger than 256 in any direction and add -cw256 flag to recon-all. Add a red warning to the reports to check the outputs carefully.

@oesteban oesteban transferred this issue from poldracklab/fmriprep Jan 8, 2019

@oesteban oesteban added the freesurfer label Jan 8, 2019

@oesteban oesteban added this to To do in 0.0.5 Jan 8, 2019

@oesteban oesteban self-assigned this Jan 8, 2019

@oesteban oesteban added the bug label Jan 8, 2019

oesteban added a commit to oesteban/smriprep that referenced this issue Jan 9, 2019

@oesteban oesteban closed this in #36 Jan 12, 2019

0.0.5 automation moved this from To do to Done Jan 12, 2019

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sandhitsu commented Mar 16, 2019

I saw the last message at #52 which says the fix for this is now available in fmriprep. However, I just tried with 1.3.0.post3 I am still getting the error

ERROR! FOV=282.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.

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