interfaces.freesurfer.registration¶
EMRegister¶
Wraps command mri_em_register
This program creates a tranform in lta format
Examples¶
>>> from nipype.interfaces.freesurfer import EMRegister
>>> register = EMRegister()
>>> register.inputs.in_file = 'norm.mgz'
>>> register.inputs.template = 'aseg.mgz'
>>> register.inputs.out_file = 'norm_transform.lta'
>>> register.inputs.skull = True
>>> register.inputs.nbrspacing = 9
>>> register.cmdline
'mri_em_register -uns 9 -skull norm.mgz aseg.mgz norm_transform.lta'
Inputs:
[Mandatory]
in_file: (an existing file name)
in brain volume
flag: %s, position: -3
template: (an existing file name)
template gca
flag: %s, position: -2
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
mask: (an existing file name)
use volume as a mask
flag: -mask %s
nbrspacing: (an integer (int or long))
align to atlas containing skull setting unknown_nbr_spacing =
nbrspacing
flag: -uns %d
num_threads: (an integer (int or long))
allows for specifying more threads
out_file: (a file name)
output transform
flag: %s, position: -1
skull: (a boolean)
align to atlas containing skull (uns=5)
flag: -skull
subjects_dir: (an existing directory name)
subjects directory
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
transform: (an existing file name)
Previously computed transform
flag: -t %s
Outputs:
out_file: (a file name)
output transform
MPRtoMNI305¶
Wraps command mpr2mni305
For complete details, see FreeSurfer documentation
Examples¶
>>> from nipype.interfaces.freesurfer import MPRtoMNI305, Info
>>> mprtomni305 = MPRtoMNI305()
>>> mprtomni305.inputs.target = 'structural.nii'
>>> mprtomni305.inputs.reference_dir = '.'
>>> mprtomni305.cmdline
'mpr2mni305 output'
>>> mprtomni305.inputs.out_file = 'struct_out'
>>> mprtomni305.cmdline
'mpr2mni305 struct_out'
>>> mprtomni305.inputs.environ['REFDIR'] == os.path.join(Info.home(), 'average')
True
>>> mprtomni305.inputs.environ['MPR2MNI305_TARGET']
'structural'
>>> mprtomni305.run()
Inputs:
[Mandatory]
reference_dir: (an existing directory name, nipype default value: )
TODO
target: (a string, nipype default value: )
input atlas file
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
in_file: (a file name, nipype default value: )
the input file prefix for MPRtoMNI305
flag: %s
subjects_dir: (an existing directory name)
subjects directory
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
log_file: (an existing file name, nipype default value:
stdout.nipype)
The output log
out_file: (a file name)
The output file '<in_file>_to_<target>_t4_vox2vox.txt'
Paint¶
Wraps command mrisp_paint
This program is useful for extracting one of the arrays (“a variable”) from a surface-registration template file. The output is a file containing a surface-worth of per-vertex values, saved in “curvature” format. Because the template data is sampled to a particular surface mesh, this conjures the idea of “painting to a surface”.
Examples¶
>>> from nipype.interfaces.freesurfer import Paint
>>> paint = Paint()
>>> paint.inputs.in_surf = 'lh.pial'
>>> paint.inputs.template = 'aseg.mgz'
>>> paint.inputs.averages = 5
>>> paint.inputs.out_file = 'lh.avg_curv'
>>> paint.cmdline
'mrisp_paint -a 5 aseg.mgz lh.pial lh.avg_curv'
Inputs:
[Mandatory]
in_surf: (an existing file name)
Surface file with grid (vertices) onto which the template data is to
be sampled or 'painted'
flag: %s, position: -2
template: (an existing file name)
Template file
flag: %s, position: -3
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
averages: (an integer (int or long))
Average curvature patterns
flag: -a %d
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
out_file: (a file name)
File containing a surface-worth of per-vertex values, saved in
'curvature' format.
flag: %s, position: -1
subjects_dir: (an existing directory name)
subjects directory
template_param: (an integer (int or long))
Frame number of the input template
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (a file name)
File containing a surface-worth of per-vertex values, saved in
'curvature' format.
Register¶
Wraps command mris_register
This program registers a surface to an average surface template.
Examples¶
>>> from nipype.interfaces.freesurfer import Register
>>> register = Register()
>>> register.inputs.in_surf = 'lh.pial'
>>> register.inputs.in_smoothwm = 'lh.pial'
>>> register.inputs.in_sulc = 'lh.pial'
>>> register.inputs.target = 'aseg.mgz'
>>> register.inputs.out_file = 'lh.pial.reg'
>>> register.inputs.curv = True
>>> register.cmdline
'mris_register -curv lh.pial aseg.mgz lh.pial.reg'
Inputs:
[Mandatory]
in_sulc: (an existing file name)
Undocumented mandatory input file
${SUBJECTS_DIR}/surf/{hemisphere}.sulc
in_surf: (an existing file name)
Surface to register, often {hemi}.sphere
flag: %s, position: -3
target: (an existing file name)
The data to register to. In normal recon-all usage, this is a
template file for average surface.
flag: %s, position: -2
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
curv: (a boolean)
Use smoothwm curvature for final alignment
flag: -curv
requires: in_smoothwm
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
in_smoothwm: (an existing file name)
Undocumented input file ${SUBJECTS_DIR}/surf/{hemisphere}.smoothwm
out_file: (a file name)
Output surface file to capture registration
flag: %s, position: -1
subjects_dir: (an existing directory name)
subjects directory
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
out_file: (a file name)
Output surface file to capture registration
RegisterAVItoTalairach¶
Wraps command avi2talxfm
converts the vox2vox from talairach_avi to a talairach.xfm file
This is a script that converts the vox2vox from talairach_avi to a talairach.xfm file. It is meant to replace the following cmd line:
tkregister2_cmdl –mov $InVol –targ $FREESURFER_HOME/average/mni305.cor.mgz –xfmout ${XFM} –vox2vox talsrcimg_to_${target}_t4_vox2vox.txt –noedit –reg talsrcimg.reg.tmp.dat set targ = $FREESURFER_HOME/average/mni305.cor.mgz set subject = mgh-02407836-v2 set InVol = $SUBJECTS_DIR/$subject/mri/orig.mgz set vox2vox = $SUBJECTS_DIR/$subject/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt
Examples¶
>>> from nipype.interfaces.freesurfer import RegisterAVItoTalairach
>>> register = RegisterAVItoTalairach()
>>> register.inputs.in_file = 'structural.mgz'
>>> register.inputs.target = 'mni305.cor.mgz'
>>> register.inputs.vox2vox = 'talsrcimg_to_structural_t4_vox2vox.txt'
>>> register.cmdline
'avi2talxfm structural.mgz mni305.cor.mgz talsrcimg_to_structural_t4_vox2vox.txt talairach.auto.xfm'
>>> register.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
The input file
flag: %s, position: 0
target: (an existing file name)
The target file
flag: %s, position: 1
vox2vox: (an existing file name)
The vox2vox file
flag: %s, position: 2
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
out_file: (a file name, nipype default value: talairach.auto.xfm)
The transform output
flag: %s, position: 3
subjects_dir: (an existing directory name)
subjects directory
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
log_file: (an existing file name, nipype default value:
stdout.nipype)
The output log
out_file: (a file name)
The output file for RegisterAVItoTalairach