Yeah, that should do the trick. Just make sure your skull-stripped
anatomical scan has the same name as your raw anatomical but with "_brain"
at the end of it. For example, if your raw anatomical is named anat.nii.gz,
then your skull-stripped anatomical should be named anat_brain.nii.gz (and
both images should be in the same directory).
Cheers,
David
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of M Mather
Sent: Wednesday, June 17, 2009 7:02 PM
To: [log in to unmask]
Subject: [FSL] FNIRT in FEAT
Hi,
Is FNIRT already implemented in FEAT?
Is it as simple as setting this setting in the design.fsf file to 1?:
# Do nonlinear registration from structural to standard space?
set fmri(regstandard_nonlinear_yn) 0
or is FNIRT something that must be run outside of feat?
Here are the settings from one of my design.fsf files:
# Registration?
set fmri(reg_yn) 1
# Registration to initial structural
set fmri(reginitial_highres_yn) 0
# Search space for registration to initial structural
# 0 : No search
# 90 : Normal search
# 180 : Full search
set fmri(reginitial_highres_search) 90
# Degrees of Freedom for registration to initial structural
set fmri(reginitial_highres_dof) 3
# Registration to main structural
set fmri(reghighres_yn) 1
# Search space for registration to main structural
# 0 : No search
# 90 : Normal search
# 180 : Full search
set fmri(reghighres_search) 90
# Degrees of Freedom for registration to main structural
set fmri(reghighres_dof) 7
# Registration to standard image?
set fmri(regstandard_yn) 1
# Standard image
set fmri(regstandard) "/Users/mm/fsl/data/standard/MNI152_T1_2mm_brain"
# Search space for registration to standard space
# 0 : No search
# 90 : Normal search
# 180 : Full search
set fmri(regstandard_search) 90
# Degrees of Freedom for registration to standard space
set fmri(regstandard_dof) 12
# Do nonlinear registration from structural to standard space?
set fmri(regstandard_nonlinear_yn) 0
# Control nonlinear warp field resolution
set fmri(regstandard_nonlinear_warpres) 10
thanks,
Mara
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