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+[common]
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+work directory = /home/data/psyinf/forrest_gump/pipe_tmp
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+data directory = /home/data/psyinf/forrest_gump/collection
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+dataset = tnt
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+
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+[subject template bold3Tp2]
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+resolution = 2.5 2.5 2.5
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+trim roi = 14 64 4 86 0 45
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+linear iterations = 2
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+skullstrip input = yes
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+final skullstrip = yes
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+#bet padding = yes
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+template bet frac = 0.3
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+#template bet gradient = 0
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+use 4d mean = yes
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+foreground threshold = 2.0
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+# must be 'no' as otherwise sub06 occ. lobe cut off gets worse
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+estimate best init template = no
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+input expression = raw/phase2/%%(subj)s/ses-.*/func/.*_bold\.nii.*
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+output base directory = %%(subj)s
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+
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+[group template grpbold3Tp2]
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+# whitespace-separated list of floats
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+resolution = 2.5 2.5 2.5
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+exclude subjects = 7 8 11 12 13
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+linear iterations = 2
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+non-linear iterations = 2
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+# whitespace-separated list of integers
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+trim roi = 2 68 2 84 8 58
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+# whitespace-separated list of integer IDs
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+final skullstrip = yes
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+subject bet frac = 0.1
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+template bet frac = 0.3
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+apply mni sform = yes
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+initial reference brain = /usr/share/data/fsl-mni152-templates/MNI152_T1_2mm_brain.nii.gz
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+input expression = raw/phase2/%%(subj)s/templates/bold3Tp2/head.nii.gz
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