Skip to content

Enh/fsl/flirt6 #537

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 6 commits into from
Apr 2, 2013
Merged

Enh/fsl/flirt6 #537

Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
f963d7f
adding fsl6 options (bbr)
Oct 24, 2012
2acc46e
typo
Oct 24, 2012
ec592ea
Merge branch 'master' into enh/fsl/flirt6
Nov 12, 2012
3e0af85
Merge branch 'master' into enh/fsl/flirt6
Dec 21, 2012
d0acea2
merge
Mar 27, 2013
d6195e9
add min version for bbr options
Mar 28, 2013
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
35 changes: 33 additions & 2 deletions nipype/interfaces/fsl/preprocess.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -407,13 +407,13 @@ class FLIRTInputSpec(FSLCommandInputSpec):
argstr='-datatype %s',
desc='force output data type')
cost = traits.Enum('mutualinfo', 'corratio', 'normcorr', 'normmi',
'leastsq', 'labeldiff',
'leastsq', 'labeldiff','bbr',
argstr='-cost %s',
desc='cost function')
# XXX What is the difference between 'cost' and 'searchcost'? Are
# these both necessary or do they map to the same variable.
cost_func = traits.Enum('mutualinfo', 'corratio', 'normcorr', 'normmi',
'leastsq', 'labeldiff',
'leastsq', 'labeldiff','bbr',
argstr='-searchcost %s',
desc='cost function')
uses_qform = traits.Bool(argstr='-usesqform',
Expand Down Expand Up @@ -475,6 +475,37 @@ class FLIRTInputSpec(FSLCommandInputSpec):
verbose = traits.Int(argstr='-verbose %d',
desc='verbose mode, 0 is least')

# BBR options
wm_seg = File(
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

for each of these please use: min_ver='5.0.0'

see: http://www.mit.edu/~satra/nipype-nightly/devel/interface_specs.html#common

argstr='-wmseg %s', min_ver='5.0.0',
desc='white matter segmentation volume needed by BBR cost function')
wmcoords = File(
argstr='-wmcoords %s', min_ver='5.0.0',
desc='white matter boundary coordinates for BBR cost function')
wmnorms = File(
argstr='-wmnorms %s', min_ver='5.0.0',
desc='white matter boundary normals for BBR cost function')
fieldmap = File(
argstr='-fieldmap %s', min_ver='5.0.0',
desc='fieldmap image in rads/s - must be already registered to the reference image')
fieldmapmask = File(
argstr='-fieldmapmask %s', min_ver='5.0.0',
desc='mask for fieldmap image')
pedir = traits.Int(
argstr='-pedir %d', min_ver='5.0.0',
desc='phase encode direction of EPI - 1/2/3=x/y/z & -1/-2/-3=-x/-y/-z')
echospacing = traits.Float(
argstr='-echospacing %f', min_ver='5.0.0',
desc='value of EPI echo spacing - units of seconds')
bbrtype = traits.Enum(
'signed', 'global_abs', 'local_abs',
argstr='-bbrtype %s', min_ver='5.0.0',
desc='type of bbr cost function: signed [default], global_abs, local_abs')
bbrslope = traits.Float(
argstr='-bbrslope %f', min_ver='5.0.0',
desc='value of bbr slope')



class FLIRTOutputSpec(TraitedSpec):
out_file = File(exists=True,
Expand Down