Releases: DCAN-Labs/dcan-macaque-pipeline
Releases · DCAN-Labs/dcan-macaque-pipeline
Hotfix - syntax error in FreeSurfer
feature update / support for new pipeline options
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PreliminaryMasking: Run ANTs N4BiasFieldCorrection on subject T1w, T2w
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FMRIVolume: Change cost function used in flirt scout-T2w reg from mutualinfo to the default cost function (correlation ratio)
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Support the following new options in nhp-abcd-bids-pipeline:
--aseg ASEG specify path to the aseg file to be used by
FreeSurfer; replaces the default aseg_acpc.nii.gz
in the subject's T1w directory. The filename of the
specified aseg file must be "aseg_acpc.nii.gz".
Default: aseg_acpc.nii.gz in subject's T1w directory
generated in PreFreeSurfer using ANTs joint label fusion.
--t1-brain-mask T1_BRAIN_MASK
specify the path to the mask file. The file specified
will be applied in place of the default masking
process in PreliminaryMasking and PreFreeSurfer.
--t2-brain-mask may be used in conjunction with this
option, but is not required.
--t2-brain-mask T2_BRAIN_MASK
specify the path to the mask file. The file specified
will be applied in place of the default masking
process in PreliminaryMasking and PreFreeSurfer.
This option may be used in conjunction with
--t1-brain-mask, but is not required.
--t1-reg-method {FLIRT_FNIRT,ANTS,ANTS_NO_INTERMEDIATE}
specify the method used to register subject T1w to
reference during PreFreeSurfer.
FLIRT_FNIRT uses FLIRT for initial affine transform
then FNIRT to register to reference.
ANTS performs intermediate registration to study
template, then registers to reference, using
antsRegistrationSyN for both.
ANTS_NO_INTERMEDIATE registers directly to reference
using antsRegistrationSyN.
Default: FLIRT_FNIRT.
--norm-gm-std-dev-scale SCALE_FACTOR
specify, as a floating-point number, the scaling factor
for the standard deviation of GM voxels in the
hypernormalized FreeSurfer T1w image relative to the
standard deviation of the adult reference image.
Reducing the standard deviation of GM voxels
may remedy issues with poor surface generation in
FreeSurfer when T1w contrast in cortical GM is uneven
or weak near the pial surface. Default = 1.
--norm-wm-std-dev-scale SCALE_FACTOR
specify, as a floating-point number, the scaling factor
for the standard deviation of WM voxels in the
hypernormalized FreeSurfer T1w image relative to the
standard deviation of the adult reference image.
Default = 1.
--norm-csf-std-dev-scale SCALE_FACTOR
specify, as a floating-point number, the scaling factor
for the standard deviation of GM voxels in the
hypernormalized FreeSurfer T1w image relative to the
standard deviation of the adult reference image.
This option has no effect when used with ADULT_GM_IP
hypernormalization. Default = 1.
--make-white-from-norm-t1
use normalized T1w volume (if it exists) as input to FreeSurfer's mris_make_surfaces when making white surfaces. Default = False.
--single-pass-pial
create pial surfaces in FreeSurfer with a single pass of mris_make_surfaces using hypernormalized T1w brain (if hypernormalization was not omitted); omits second pass of mris_make_surfaces (in which the surfaces generated in
the first pass would be used as priors, and a
non-hypernormalized T1w brain is used). Default = False.
Remove BASH set -e
BASH set -e was causing halting when that is not the desired behavior given the small temporary MATLAB folder existence error occurring.
Add in Bene's fixes
See commit e31ab3a
Fix: apply matrix to head - was messing up the brain and mask before.
v0.0.1 Update README.md
Initial public release
v0.0.0 Initial public release; from gitlab d6d6497309e341d05c7afcb501e7d0fe6…