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Generating MAGeTbrain Quality Control Images

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Gabriel A. Devenyi edited this page Apr 26, 2019 · 2 revisions

After finishing MAGeT Brain, you can produce PNG/JPG images of each subject for QC. A script is available from minc-toolkit-extras or module load minc-toolkit-extras

From here, the format of the command is:

$ MAGeT-QC.sh <input subject file> <input label file> <output qc image>

Example:

$ MAGeT-QC.sh input/subjects/brains/subject1_t1.n4correct.cutneckapplyautocrop.lsq6.mnc output/fusion/majority_vote/subject1_t1.n4correct.cutneckapplyautocrop.lsq6_labels.mnc QC/subject1_t1.n4correct.cutneckapplyautocrop.lsq6.jpg

And the result: 82007000_t1 n4correct cutneckapplyautocrop beastextract lsq6_labels

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