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- [common]
- work directory = /home/data/psyinf/forrest_gump/pipe_tmp
- data directory = /home/data/psyinf/forrest_gump/collection
- dataset = tnt
- [subject template bold3Tp2]
- resolution = 2.5 2.5 2.5
- trim roi = 14 64 4 86 0 45
- linear iterations = 2
- skullstrip input = yes
- final skullstrip = yes
- #bet padding = yes
- template bet frac = 0.3
- #template bet gradient = 0
- use 4d mean = yes
- foreground threshold = 2.0
- # must be 'no' as otherwise sub06 occ. lobe cut off gets worse
- estimate best init template = no
- input expression = raw/phase2/%%(subj)s/ses-.*/func/.*_bold\.nii.*
- output base directory = %%(subj)s
- [group template grpbold3Tp2]
- # whitespace-separated list of floats
- resolution = 2.5 2.5 2.5
- linear iterations = 2
- non-linear iterations = 2
- # whitespace-separated list of integers
- trim roi = 2 68 2 84 8 58
- # whitespace-separated list of integer IDs
- final skullstrip = yes
- subject bet frac = 0.1
- template bet frac = 0.3
- apply mni sform = yes
- initial reference brain = /usr/share/data/fsl-mni152-templates/MNI152_T1_2mm_brain.nii.gz
- input expression = %%(subj)s/bold3Tp2/head.nii.gz
- [align2tmpl subjbold3Tp2_to_grpbold3Tp2]
- template = grpbold3Tp2
- input expression = %%(subj)s/bold3Tp2/head\.nii.*
- search radius = 15
- non-linear = yes
- use qform = yes
- warp resolution = 10
- motion correction = False
- input is subject template = yes
- [subject template bold7Tp1]
- resolution = 1.2 1.2 1.2
- trim roi = 10 160 0 186 27 48
- linear iterations = 2
- final skullstrip = yes
- bet padding = yes
- template bet frac = 0.12
- template bet gradient = 0
- zslice padding = 80
- use 4d mean = no
- foreground threshold = 2.0
- input expression = raw/phase1/%%(subj)s/BOLD/task00[1,2]*_run.*/bold_dico\.nii.*
- output base directory = %%(subj)s
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