interfaces.freesurfer.preprocess¶
ApplyVolTransform¶
Wraps command mri_vol2vol
Use FreeSurfer mri_vol2vol to apply a transform.
Examples¶
>>> from nipype.interfaces.freesurfer import ApplyVolTransform
>>> applyreg = ApplyVolTransform()
>>> applyreg.inputs.source_file = 'structural.nii'
>>> applyreg.inputs.reg_file = 'register.dat'
>>> applyreg.inputs.transformed_file = 'struct_warped.nii'
>>> applyreg.inputs.fs_target = True
>>> applyreg.cmdline
'mri_vol2vol --fstarg --reg register.dat --mov structural.nii --o struct_warped.nii'
Inputs:
[Mandatory]
fs_target: (a boolean)
use orig.mgz from subject in regfile as target
flag: --fstarg
mutually_exclusive: target_file, tal, fs_target
requires: reg_file
fsl_reg_file: (an existing file name)
fslRAS-to-fslRAS matrix (FSL format)
flag: --fsl %s
mutually_exclusive: reg_file, fsl_reg_file, xfm_reg_file,
reg_header, subject
reg_file: (an existing file name)
tkRAS-to-tkRAS matrix (tkregister2 format)
flag: --reg %s
mutually_exclusive: reg_file, fsl_reg_file, xfm_reg_file,
reg_header, subject
reg_header: (a boolean)
ScannerRAS-to-ScannerRAS matrix = identity
flag: --regheader
mutually_exclusive: reg_file, fsl_reg_file, xfm_reg_file,
reg_header, subject
source_file: (an existing file name)
Input volume you wish to transform
flag: --mov %s
subject: (a string)
set matrix = identity and use subject for any templates
flag: --s %s
mutually_exclusive: reg_file, fsl_reg_file, xfm_reg_file,
reg_header, subject
tal: (a boolean)
map to a sub FOV of MNI305 (with --reg only)
flag: --tal
mutually_exclusive: target_file, tal, fs_target
target_file: (an existing file name)
Output template volume
flag: --targ %s
mutually_exclusive: target_file, tal, fs_target
xfm_reg_file: (an existing file name)
ScannerRAS-to-ScannerRAS matrix (MNI format)
flag: --xfm %s
mutually_exclusive: reg_file, fsl_reg_file, xfm_reg_file,
reg_header, subject
[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
interp: ('trilin' or 'nearest' or 'cubic')
Interpolation method (<trilin> or nearest)
flag: --interp %s
inverse: (a boolean)
sample from target to source
flag: --inv
invert_morph: (a boolean)
Compute and use the inverse of the non-linear morph to resample the
input volume. To be used by --m3z.
flag: --inv-morph
requires: m3z_file
m3z_file: (a file name)
This is the morph to be applied to the volume. Unless the morph is
in mri/transforms (eg.: for talairach.m3z computed by reconall), you
will need to specify the full path to this morph and use the
--noDefM3zPath flag.
flag: --m3z %s
no_ded_m3z_path: (a boolean)
To be used with the m3z flag. Instructs the code not to look for
them3z morph in the default location
(SUBJECTS_DIR/subj/mri/transforms), but instead just use the path
indicated in --m3z.
flag: --noDefM3zPath
requires: m3z_file
no_resample: (a boolean)
Do not resample; just change vox2ras matrix
flag: --no-resample
subjects_dir: (an existing directory name)
subjects directory
tal_resolution: (a float)
Resolution to sample when using tal
flag: --talres %.10f
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
transformed_file: (a file name)
Output volume
flag: --o %s
Outputs:
transformed_file: (an existing file name)
Path to output file if used normally
BBRegister¶
Wraps command bbregister
Use FreeSurfer bbregister to register a volume to the Freesurfer anatomical.
This program performs within-subject, cross-modal registration using a boundary-based cost function. The registration is constrained to be 6 DOF (rigid). It is required that you have an anatomical scan of the subject that has already been recon-all-ed using freesurfer.
Examples¶
>>> from nipype.interfaces.freesurfer import BBRegister
>>> bbreg = BBRegister(subject_id='me', source_file='structural.nii', init='header', contrast_type='t2')
>>> bbreg.cmdline
'bbregister --t2 --init-header --reg structural_bbreg_me.dat --mov structural.nii --s me'
Inputs:
[Mandatory]
contrast_type: ('t1' or 't2')
contrast type of image
flag: --%s
init: ('spm' or 'fsl' or 'header')
initialize registration spm, fsl, header
flag: --init-%s
mutually_exclusive: init_reg_file
init_reg_file: (an existing file name)
existing registration file
flag: --init-reg %s
mutually_exclusive: init
source_file: (a file name)
source file to be registered
flag: --mov %s
subject_id: (a string)
freesurfer subject id
flag: --s %s
[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
epi_mask: (a boolean)
mask out B0 regions in stages 1 and 2
flag: --epi-mask
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
intermediate_file: (an existing file name)
Intermediate image, e.g. in case of partial FOV
flag: --int %s
out_fsl_file: (a boolean or a file name)
write the transformation matrix in FSL FLIRT format
flag: --fslmat %s
out_reg_file: (a file name)
output registration file
flag: --reg %s
reg_frame: (an integer (int or long))
0-based frame index for 4D source file
flag: --frame %d
mutually_exclusive: reg_middle_frame
reg_middle_frame: (a boolean)
Register middle frame of 4D source file
flag: --mid-frame
mutually_exclusive: reg_frame
registered_file: (a boolean or a file name)
output warped sourcefile either True or filename
flag: --o %s
spm_nifti: (a boolean)
force use of nifti rather than analyze with SPM
flag: --spm-nii
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:
min_cost_file: (an existing file name)
Output registration minimum cost file
out_fsl_file: (a file name)
Output FLIRT-style registration file
out_reg_file: (an existing file name)
Output registration file
registered_file: (a file name)
Registered and resampled source file
DICOMConvert¶
Wraps command mri_convert
use fs mri_convert to convert dicom files
Examples¶
>>> from nipype.interfaces.freesurfer import DICOMConvert
>>> cvt = DICOMConvert()
>>> cvt.inputs.dicom_dir = 'dicomdir'
>>> cvt.inputs.file_mapping = [('nifti', '*.nii'), ('info', 'dicom*.txt'), ('dti', '*dti.bv*')]
Inputs:
[Mandatory]
base_output_dir: (a directory name)
directory in which subject directories are created
dicom_dir: (an existing directory name)
dicom directory from which to convert dicom files
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
dicom_info: (an existing file name)
File containing summary information from mri_parse_sdcmdir
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
file_mapping: (a list of items which are a tuple of the form: (a
string, a string))
defines the output fields of interface
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
ignore_single_slice: (a boolean)
ignore volumes containing a single slice
requires: dicom_info
out_type: ('cor' or 'mgh' or 'mgz' or 'minc' or 'analyze' or
'analyze4d' or 'spm' or 'afni' or 'brik' or 'bshort' or 'bfloat' or
'sdt' or 'outline' or 'otl' or 'gdf' or 'nifti1' or 'nii' or
'niigz', nipype default value: niigz)
defines the type of output file produced
seq_list: (a list of items which are a string)
list of pulse sequence names to be converted.
requires: dicom_info
subject_dir_template: (a string, nipype default value: S.%04d)
template for subject directory name
subject_id: (any value)
subject identifier to insert into template
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:
None
FitMSParams¶
Wraps command mri_ms_fitparms
Estimate tissue paramaters from a set of FLASH images.
Examples¶
>>> from nipype.interfaces.freesurfer import FitMSParams
>>> msfit = FitMSParams()
>>> msfit.inputs.in_files = ['flash_05.mgz', 'flash_30.mgz']
>>> msfit.inputs.out_dir = 'flash_parameters'
>>> msfit.cmdline
'mri_ms_fitparms flash_05.mgz flash_30.mgz flash_parameters'
Inputs:
[Mandatory]
in_files: (a list of items which are an existing file name)
list of FLASH images (must be in mgh format)
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
flip_list: (a list of items which are an integer (int or long))
list of flip angles of the input files
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_dir: (a directory name)
directory to store output in
flag: %s, position: -1
subjects_dir: (an existing directory name)
subjects directory
te_list: (a list of items which are a float)
list of TEs of the input files (in msec)
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
tr_list: (a list of items which are an integer (int or long))
list of TRs of the input files (in msec)
xfm_list: (a list of items which are an existing file name)
list of transform files to apply to each FLASH image
Outputs:
pd_image: (an existing file name)
image of estimated proton density values
t1_image: (an existing file name)
image of estimated T1 relaxation values
t2star_image: (an existing file name)
image of estimated T2* values
MRIConvert¶
Wraps command mri_convert
use fs mri_convert to manipulate files
Note
Adds niigz as an output type option
Examples¶
>>> mc = MRIConvert()
>>> mc.inputs.in_file = 'structural.nii'
>>> mc.inputs.out_file = 'outfile.mgz'
>>> mc.inputs.out_type = 'mgz'
>>> mc.cmdline
'mri_convert --out_type mgz --input_volume structural.nii --output_volume outfile.mgz'
Inputs:
[Mandatory]
in_file: (an existing file name)
File to read/convert
flag: --input_volume %s, position: -2
[Optional]
apply_inv_transform: (an existing file name)
apply inverse transformation xfm file
flag: --apply_inverse_transform %s
apply_transform: (an existing file name)
apply xfm file
flag: --apply_transform %s
args: (a string)
Additional parameters to the command
flag: %s
ascii: (a boolean)
save output as ascii col>row>slice>frame
flag: --ascii
autoalign_matrix: (an existing file name)
text file with autoalign matrix
flag: --autoalign %s
color_file: (an existing file name)
color file
flag: --color_file %s
conform: (a boolean)
conform to 256^3
flag: --conform
conform_min: (a boolean)
conform to smallest size
flag: --conform_min
conform_size: (a float)
conform to size_in_mm
flag: --conform_size %s
crop_center: (a tuple of the form: (an integer (int or long), an
integer (int or long), an integer (int or long)))
<x> <y> <z> crop to 256 around center (x, y, z)
flag: --crop %d %d %d
crop_gdf: (a boolean)
apply GDF cropping
flag: --crop_gdf
crop_size: (a tuple of the form: (an integer (int or long), an
integer (int or long), an integer (int or long)))
<dx> <dy> <dz> crop to size <dx, dy, dz>
flag: --cropsize %d %d %d
cut_ends: (an integer (int or long))
remove ncut slices from the ends
flag: --cutends %d
devolve_transform: (a string)
subject id
flag: --devolvexfm %s
drop_n: (an integer (int or long))
drop the last n frames
flag: --ndrop %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
fill_parcellation: (a boolean)
fill parcellation
flag: --fill_parcellation
force_ras: (a boolean)
use default when orientation info absent
flag: --force_ras_good
frame: (an integer (int or long))
keep only 0-based frame number
flag: --frame %d
frame_subsample: (a tuple of the form: (an integer (int or long), an
integer (int or long), an integer (int or long)))
start delta end : frame subsampling (end = -1 for end)
flag: --fsubsample %d %d %d
fwhm: (a float)
smooth input volume by fwhm mm
flag: --fwhm %f
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_center: (a list of at most 3 items which are a float)
<R coordinate> <A coordinate> <S coordinate>
flag: --in_center %s
in_i_dir: (a tuple of the form: (a float, a float, a float))
<R direction> <A direction> <S direction>
flag: --in_i_direction %f %f %f
in_i_size: (an integer (int or long))
input i size
flag: --in_i_size %d
in_info: (a boolean)
display input info
flag: --in_info
in_j_dir: (a tuple of the form: (a float, a float, a float))
<R direction> <A direction> <S direction>
flag: --in_j_direction %f %f %f
in_j_size: (an integer (int or long))
input j size
flag: --in_j_size %d
in_k_dir: (a tuple of the form: (a float, a float, a float))
<R direction> <A direction> <S direction>
flag: --in_k_direction %f %f %f
in_k_size: (an integer (int or long))
input k size
flag: --in_k_size %d
in_like: (an existing file name)
input looks like
flag: --in_like %s
in_matrix: (a boolean)
display input matrix
flag: --in_matrix
in_orientation: ('LAI' or 'LIA' or 'ALI' or 'AIL' or 'ILA' or 'IAL'
or 'LAS' or 'LSA' or 'ALS' or 'ASL' or 'SLA' or 'SAL' or 'LPI' or
'LIP' or 'PLI' or 'PIL' or 'ILP' or 'IPL' or 'LPS' or 'LSP' or
'PLS' or 'PSL' or 'SLP' or 'SPL' or 'RAI' or 'RIA' or 'ARI' or
'AIR' or 'IRA' or 'IAR' or 'RAS' or 'RSA' or 'ARS' or 'ASR' or
'SRA' or 'SAR' or 'RPI' or 'RIP' or 'PRI' or 'PIR' or 'IRP' or
'IPR' or 'RPS' or 'RSP' or 'PRS' or 'PSR' or 'SRP' or 'SPR')
specify the input orientation
flag: --in_orientation %s
in_scale: (a float)
input intensity scale factor
flag: --scale %f
in_stats: (a boolean)
display input stats
flag: --in_stats
in_type: ('cor' or 'mgh' or 'mgz' or 'minc' or 'analyze' or
'analyze4d' or 'spm' or 'afni' or 'brik' or 'bshort' or 'bfloat' or
'sdt' or 'outline' or 'otl' or 'gdf' or 'nifti1' or 'nii' or
'niigz' or 'ge' or 'gelx' or 'lx' or 'ximg' or 'siemens' or 'dicom'
or 'siemens_dicom')
input file type
flag: --in_type %s
invert_contrast: (a float)
threshold for inversting contrast
flag: --invert_contrast %f
midframe: (a boolean)
keep only the middle frame
flag: --mid-frame
no_change: (a boolean)
don't change type of input to that of template
flag: --nochange
no_scale: (a boolean)
dont rescale values for COR
flag: --no_scale 1
no_translate: (a boolean)
~~~
flag: --no_translate
no_write: (a boolean)
do not write output
flag: --no_write
out_center: (a tuple of the form: (a float, a float, a float))
<R coordinate> <A coordinate> <S coordinate>
flag: --out_center %f %f %f
out_datatype: ('uchar' or 'short' or 'int' or 'float')
output data type <uchar|short|int|float>
flag: --out_data_type %s
out_file: (a file name)
output filename or True to generate one
flag: --output_volume %s, position: -1
out_i_count: (an integer (int or long))
some count ?? in i direction
flag: --out_i_count %d
out_i_dir: (a tuple of the form: (a float, a float, a float))
<R direction> <A direction> <S direction>
flag: --out_i_direction %f %f %f
out_i_size: (an integer (int or long))
output i size
flag: --out_i_size %d
out_info: (a boolean)
display output info
flag: --out_info
out_j_count: (an integer (int or long))
some count ?? in j direction
flag: --out_j_count %d
out_j_dir: (a tuple of the form: (a float, a float, a float))
<R direction> <A direction> <S direction>
flag: --out_j_direction %f %f %f
out_j_size: (an integer (int or long))
output j size
flag: --out_j_size %d
out_k_count: (an integer (int or long))
some count ?? in k direction
flag: --out_k_count %d
out_k_dir: (a tuple of the form: (a float, a float, a float))
<R direction> <A direction> <S direction>
flag: --out_k_direction %f %f %f
out_k_size: (an integer (int or long))
output k size
flag: --out_k_size %d
out_matrix: (a boolean)
display output matrix
flag: --out_matrix
out_orientation: ('LAI' or 'LIA' or 'ALI' or 'AIL' or 'ILA' or 'IAL'
or 'LAS' or 'LSA' or 'ALS' or 'ASL' or 'SLA' or 'SAL' or 'LPI' or
'LIP' or 'PLI' or 'PIL' or 'ILP' or 'IPL' or 'LPS' or 'LSP' or
'PLS' or 'PSL' or 'SLP' or 'SPL' or 'RAI' or 'RIA' or 'ARI' or
'AIR' or 'IRA' or 'IAR' or 'RAS' or 'RSA' or 'ARS' or 'ASR' or
'SRA' or 'SAR' or 'RPI' or 'RIP' or 'PRI' or 'PIR' or 'IRP' or
'IPR' or 'RPS' or 'RSP' or 'PRS' or 'PSR' or 'SRP' or 'SPR')
specify the output orientation
flag: --out_orientation %s
out_scale: (a float)
output intensity scale factor
flag: --out-scale %d
out_stats: (a boolean)
display output stats
flag: --out_stats
out_type: ('cor' or 'mgh' or 'mgz' or 'minc' or 'analyze' or
'analyze4d' or 'spm' or 'afni' or 'brik' or 'bshort' or 'bfloat' or
'sdt' or 'outline' or 'otl' or 'gdf' or 'nifti1' or 'nii' or
'niigz')
output file type
flag: --out_type %s
parse_only: (a boolean)
parse input only
flag: --parse_only
read_only: (a boolean)
read the input volume
flag: --read_only
reorder: (a tuple of the form: (an integer (int or long), an integer
(int or long), an integer (int or long)))
olddim1 olddim2 olddim3
flag: --reorder %d %d %d
resample_type: ('interpolate' or 'weighted' or 'nearest' or 'sinc' or
'cubic')
<interpolate|weighted|nearest|sinc|cubic> (default is interpolate)
flag: --resample_type %s
reslice_like: (an existing file name)
reslice output to match file
flag: --reslice_like %s
sdcm_list: (an existing file name)
list of DICOM files for conversion
flag: --sdcmlist %s
skip_n: (an integer (int or long))
skip the first n frames
flag: --nskip %d
slice_bias: (a float)
apply half-cosine bias field
flag: --slice-bias %f
slice_crop: (a tuple of the form: (an integer (int or long), an
integer (int or long)))
s_start s_end : keep slices s_start to s_end
flag: --slice-crop %d %d
slice_reverse: (a boolean)
reverse order of slices, update vox2ras
flag: --slice-reverse
smooth_parcellation: (a boolean)
smooth parcellation
flag: --smooth_parcellation
sphinx: (a boolean)
change orientation info to sphinx
flag: --sphinx
split: (a boolean)
split output frames into separate output files.
flag: --split
status_file: (a file name)
status file for DICOM conversion
flag: --status %s
subject_name: (a string)
subject name ???
flag: --subject_name %s
subjects_dir: (an existing directory name)
subjects directory
te: (an integer (int or long))
TE in msec
flag: -te %d
template_info: (a boolean)
dump info about template
template_type: ('cor' or 'mgh' or 'mgz' or 'minc' or 'analyze' or
'analyze4d' or 'spm' or 'afni' or 'brik' or 'bshort' or 'bfloat' or
'sdt' or 'outline' or 'otl' or 'gdf' or 'nifti1' or 'nii' or
'niigz' or 'ge' or 'gelx' or 'lx' or 'ximg' or 'siemens' or 'dicom'
or 'siemens_dicom')
template file type
flag: --template_type %s
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
ti: (an integer (int or long))
TI in msec (note upper case flag)
flag: -ti %d
tr: (an integer (int or long))
TR in msec
flag: -tr %d
unwarp_gradient: (a boolean)
unwarp gradient nonlinearity
flag: --unwarp_gradient_nonlinearity
vox_size: (a tuple of the form: (a float, a float, a float))
<size_x> <size_y> <size_z> specify the size (mm) - useful for
upsampling or downsampling
flag: -voxsize %f %f %f
zero_ge_z_offset: (a boolean)
zero ge z offset ???
flag: --zero_ge_z_offset
zero_outlines: (a boolean)
zero outlines
flag: --zero_outlines
Outputs:
out_file: (a list of items which are an existing file name)
converted output file
ParseDICOMDir¶
Wraps command mri_parse_sdcmdir
Uses mri_parse_sdcmdir to get information from dicom directories
Examples¶
>>> from nipype.interfaces.freesurfer import ParseDICOMDir
>>> dcminfo = ParseDICOMDir()
>>> dcminfo.inputs.dicom_dir = '.'
>>> dcminfo.inputs.sortbyrun = True
>>> dcminfo.inputs.summarize = True
>>> dcminfo.cmdline
'mri_parse_sdcmdir --d . --o dicominfo.txt --sortbyrun --summarize'
Inputs:
[Mandatory]
dicom_dir: (an existing directory name)
path to siemens dicom directory
flag: --d %s
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
dicom_info_file: (a file name, nipype default value: dicominfo.txt)
file to which results are written
flag: --o %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
sortbyrun: (a boolean)
assign run numbers
flag: --sortbyrun
subjects_dir: (an existing directory name)
subjects directory
summarize: (a boolean)
only print out info for run leaders
flag: --summarize
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:
dicom_info_file: (an existing file name)
text file containing dicom information
ReconAll¶
Wraps command recon-all
Uses recon-all to generate surfaces and parcellations of structural data from anatomical images of a subject.
Examples¶
>>> from nipype.interfaces.freesurfer import ReconAll
>>> reconall = ReconAll()
>>> reconall.inputs.subject_id = 'foo'
>>> reconall.inputs.directive = 'all'
>>> reconall.inputs.subjects_dir = '.'
>>> reconall.inputs.T1_files = 'structural.nii'
>>> reconall.cmdline
'recon-all -all -i structural.nii -subjid foo -sd .'
Inputs:
[Mandatory]
[Optional]
T1_files: (a list of items which are an existing file name)
name of T1 file to process
flag: -i %s...
T2_file: (an existing file name)
Use a T2 image to refine the cortical surface
flag: -T2 %s
args: (a string)
Additional parameters to the command
flag: %s
directive: ('all' or 'autorecon1' or 'autorecon2' or 'autorecon2-cp'
or 'autorecon2-wm' or 'autorecon2-inflate1' or 'autorecon2-perhemi'
or 'autorecon3' or 'localGI' or 'qcache', nipype default value:
all)
process directive
flag: -%s, position: 0
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
flags: (a string)
additional parameters
flag: %s
hemi: ('lh' or 'rh')
hemisphere to process
flag: -hemi %s
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
openmp: (an integer (int or long))
Number of processors to use in parallel
flag: -openmp %d
subject_id: (a string, nipype default value: recon_all)
subject name
flag: -subjid %s
subjects_dir: (an existing directory name)
path to subjects directory
flag: -sd %s
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:
BA_stats: (a list of items which are an existing file name)
Brodmann Area statistics files
T1: (an existing file name)
Intensity normalized whole-head volume
annot: (a list of items which are an existing file name)
Surface annotation files
aparc_a2009s_stats: (a list of items which are an existing file name)
Aparc a2009s parcellation statistics files
aparc_aseg: (a list of items which are an existing file name)
Aparc parcellation projected into aseg volume
aparc_stats: (a list of items which are an existing file name)
Aparc parcellation statistics files
aseg: (an existing file name)
Volumetric map of regions from automatic segmentation
aseg_stats: (a list of items which are an existing file name)
Automated segmentation statistics file
brain: (an existing file name)
Intensity normalized brain-only volume
brainmask: (an existing file name)
Skull-stripped (brain-only) volume
curv: (a list of items which are an existing file name)
Maps of surface curvature
curv_stats: (a list of items which are an existing file name)
Curvature statistics files
entorhinal_exvivo_stats: (a list of items which are an existing file
name)
Entorhinal exvivo statistics files
filled: (an existing file name)
Subcortical mass volume
inflated: (a list of items which are an existing file name)
Inflated surface meshes
label: (a list of items which are an existing file name)
Volume and surface label files
norm: (an existing file name)
Normalized skull-stripped volume
nu: (an existing file name)
Non-uniformity corrected whole-head volume
orig: (an existing file name)
Base image conformed to Freesurfer space
pial: (a list of items which are an existing file name)
Gray matter/pia mater surface meshes
rawavg: (an existing file name)
Volume formed by averaging input images
ribbon: (a list of items which are an existing file name)
Volumetric maps of cortical ribbons
smoothwm: (a list of items which are an existing file name)
Smoothed original surface meshes
sphere: (a list of items which are an existing file name)
Spherical surface meshes
sphere_reg: (a list of items which are an existing file name)
Spherical registration file
subject_id: (a string)
Subject name for whom to retrieve data
subjects_dir: (an existing directory name)
Freesurfer subjects directory.
sulc: (a list of items which are an existing file name)
Surface maps of sulcal depth
thickness: (a list of items which are an existing file name)
Surface maps of cortical thickness
volume: (a list of items which are an existing file name)
Surface maps of cortical volume
white: (a list of items which are an existing file name)
White/gray matter surface meshes
wm: (an existing file name)
Segmented white-matter volume
wmparc: (an existing file name)
Aparc parcellation projected into subcortical white matter
wmparc_stats: (a list of items which are an existing file name)
White matter parcellation statistics file
Resample¶
Wraps command mri_convert
Use FreeSurfer mri_convert to up or down-sample image files
Examples¶
>>> from nipype.interfaces import freesurfer
>>> resampler = freesurfer.Resample()
>>> resampler.inputs.in_file = 'structural.nii'
>>> resampler.inputs.resampled_file = 'resampled.nii'
>>> resampler.inputs.voxel_size = (2.1, 2.1, 2.1)
>>> resampler.cmdline
'mri_convert -vs 2.10 2.10 2.10 -i structural.nii -o resampled.nii'
Inputs:
[Mandatory]
in_file: (an existing file name)
file to resample
flag: -i %s, position: -2
voxel_size: (a tuple of the form: (a float, a float, a float))
triplet of output voxel sizes
flag: -vs %.2f %.2f %.2f
[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
resampled_file: (a file name)
output filename
flag: -o %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:
resampled_file: (an existing file name)
output filename
RobustRegister¶
Wraps command mri_robust_register
Perform intramodal linear registration (translation and rotation) using robust statistics.
Examples¶
>>> from nipype.interfaces.freesurfer import RobustRegister
>>> reg = RobustRegister()
>>> reg.inputs.source_file = 'structural.nii'
>>> reg.inputs.target_file = 'T1.nii'
>>> reg.inputs.auto_sens = True
>>> reg.inputs.init_orient = True
>>> reg.cmdline
'mri_robust_register --satit --initorient --lta structural_robustreg.lta --mov structural.nii --dst T1.nii'
References¶
Reuter, M, Rosas, HD, and Fischl, B, (2010). Highly Accurate Inverse Consistent Registration: A Robust Approach. Neuroimage 53(4) 1181-96.
Inputs:
[Mandatory]
auto_sens: (a boolean)
auto-detect good sensitivity
flag: --satit
mutually_exclusive: outlier_sens
outlier_sens: (a float)
set outlier sensitivity explicitly
flag: --sat %.4f
mutually_exclusive: auto_sens
source_file: (a file name)
volume to be registered
flag: --mov %s
target_file: (a file name)
target volume for the registration
flag: --dst %s
[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
est_int_scale: (a boolean)
estimate intensity scale (recommended for unnormalized images)
flag: --iscale
force_double: (a boolean)
use double-precision intensities
flag: --doubleprec
force_float: (a boolean)
use float intensities
flag: --floattype
half_source: (a boolean or a file name)
write source volume mapped to halfway space
flag: --halfmov %s
half_source_xfm: (a boolean or a file name)
write transform from source to halfway space
flag: --halfmovlta %s
half_targ: (a boolean or a file name)
write target volume mapped to halfway space
flag: --halfdst %s
half_targ_xfm: (a boolean or a file name)
write transform from target to halfway space
flag: --halfdstlta %s
half_weights: (a boolean or a file name)
write weights volume mapped to halfway space
flag: --halfweights %s
high_iterations: (an integer (int or long))
max # of times on highest resolution
flag: --highit %d
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_xfm_file: (an existing file name)
use initial transform on source
flag: --transform
init_orient: (a boolean)
use moments for initial orient (recommended for stripped brains)
flag: --initorient
iteration_thresh: (a float)
stop iterations when below threshold
flag: --epsit %.3f
least_squares: (a boolean)
use least squares instead of robust estimator
flag: --leastsquares
mask_source: (an existing file name)
image to mask source volume with
flag: --maskmov %s
mask_target: (an existing file name)
image to mask target volume with
flag: --maskdst %s
max_iterations: (an integer (int or long))
maximum # of times on each resolution
flag: --maxit %d
no_init: (a boolean)
skip transform init
flag: --noinit
no_multi: (a boolean)
work on highest resolution
flag: --nomulti
out_reg_file: (a file name)
registration file to write
flag: --lta %s
outlier_limit: (a float)
set maximal outlier limit in satit
flag: --wlimit %.3f
registered_file: (a boolean or a file name)
registered image; either True or filename
flag: --warp %s
subjects_dir: (an existing directory name)
subjects directory
subsample_thresh: (an integer (int or long))
subsample if dimension is above threshold size
flag: --subsample %d
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
trans_only: (a boolean)
find 3 parameter translation only
flag: --transonly
weights_file: (a boolean or a file name)
weights image to write; either True or filename
flag: --weights %s
write_vo2vox: (a boolean)
output vox2vox matrix (default is RAS2RAS)
flag: --vox2vox
Outputs:
half_source: (a file name)
source image mapped to halfway space
half_source_xfm: (a file name)
transform file to map source image to halfway space
half_targ: (a file name)
target image mapped to halfway space
half_targ_xfm: (a file name)
transform file to map target image to halfway space
half_weights: (a file name)
weights image mapped to halfway space
out_reg_file: (an existing file name)
output registration file
registered_file: (a file name)
output image with registration applied
weights_file: (a file name)
image of weights used
Smooth¶
Wraps command mris_volsmooth
Use FreeSurfer mris_volsmooth to smooth a volume
This function smoothes cortical regions on a surface and non-cortical regions in volume.
Note
Cortical voxels are mapped to the surface (3D->2D) and then the smoothed values from the surface are put back into the volume to fill the cortical ribbon. If data is smoothed with this algorithm, one has to be careful about how further processing is interpreted.
Examples¶
>>> from nipype.interfaces.freesurfer import Smooth
>>> smoothvol = Smooth(in_file='functional.nii', smoothed_file = 'foo_out.nii', reg_file='register.dat', surface_fwhm=10, vol_fwhm=6)
>>> smoothvol.cmdline
'mris_volsmooth --i functional.nii --reg register.dat --o foo_out.nii --fwhm 10.000000 --vol-fwhm 6.000000'
Inputs:
[Mandatory]
in_file: (an existing file name)
source volume
flag: --i %s
num_iters: (an integer >= 1)
number of iterations instead of fwhm
flag: --niters %d
mutually_exclusive: surface_fwhm
reg_file: (an existing file name)
registers volume to surface anatomical
flag: --reg %s
surface_fwhm: (a floating point number >= 0.0)
surface FWHM in mm
flag: --fwhm %f
mutually_exclusive: num_iters
requires: reg_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
proj_frac: (a float)
project frac of thickness a long surface normal
flag: --projfrac %s
mutually_exclusive: proj_frac_avg
proj_frac_avg: (a tuple of the form: (a float, a float, a float))
average a long normal min max delta
flag: --projfrac-avg %.2f %.2f %.2f
mutually_exclusive: proj_frac
smoothed_file: (a file name)
output volume
flag: --o %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
vol_fwhm: (a floating point number >= 0.0)
volume smoothing outside of surface
flag: --vol-fwhm %f
Outputs:
smoothed_file: (an existing file name)
smoothed input volume
SynthesizeFLASH¶
Wraps command mri_synthesize
Synthesize a FLASH acquisition from T1 and proton density maps.
Examples¶
>>> from nipype.interfaces.freesurfer import SynthesizeFLASH
>>> syn = SynthesizeFLASH(tr=20, te=3, flip_angle=30)
>>> syn.inputs.t1_image = 'T1.mgz'
>>> syn.inputs.pd_image = 'PD.mgz'
>>> syn.inputs.out_file = 'flash_30syn.mgz'
>>> syn.cmdline
'mri_synthesize 20.00 30.00 3.000 T1.mgz PD.mgz flash_30syn.mgz'
Inputs:
[Mandatory]
flip_angle: (a float)
flip angle (in degrees)
flag: %.2f, position: 3
pd_image: (an existing file name)
image of proton density values
flag: %s, position: 6
t1_image: (an existing file name)
image of T1 values
flag: %s, position: 5
te: (a float)
echo time (in msec)
flag: %.3f, position: 4
tr: (a float)
repetition time (in msec)
flag: %.2f, 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
fixed_weighting: (a boolean)
use a fixed weighting to generate optimal gray/white contrast
flag: -w, position: 1
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)
image to write
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:
out_file: (an existing file name)
synthesized FLASH acquisition
UnpackSDICOMDir¶
Wraps command unpacksdcmdir
Use unpacksdcmdir to convert dicom files
Call unpacksdcmdir -help from the command line to see more information on using this command.
Examples¶
>>> from nipype.interfaces.freesurfer import UnpackSDICOMDir
>>> unpack = UnpackSDICOMDir()
>>> unpack.inputs.source_dir = '.'
>>> unpack.inputs.output_dir = '.'
>>> unpack.inputs.run_info = (5, 'mprage', 'nii', 'struct')
>>> unpack.inputs.dir_structure = 'generic'
>>> unpack.cmdline
'unpacksdcmdir -generic -targ . -run 5 mprage nii struct -src .'
Inputs:
[Mandatory]
config: (an existing file name)
specify unpacking rules in file
flag: -cfg %s
mutually_exclusive: run_info, config, seq_config
run_info: (a tuple of the form: (an integer (int or long), a string,
a string, a string))
runno subdir format name : spec unpacking rules on cmdline
flag: -run %d %s %s %s
mutually_exclusive: run_info, config, seq_config
seq_config: (an existing file name)
specify unpacking rules based on sequence
flag: -seqcfg %s
mutually_exclusive: run_info, config, seq_config
source_dir: (an existing directory name)
directory with the DICOM files
flag: -src %s
[Optional]
args: (a string)
Additional parameters to the command
flag: %s
dir_structure: ('fsfast' or 'generic')
unpack to specified directory structures
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
log_file: (an existing file name)
explicilty set log file
flag: -log %s
no_info_dump: (a boolean)
do not create infodump file
flag: -noinfodump
no_unpack_err: (a boolean)
do not try to unpack runs with errors
flag: -no-unpackerr
output_dir: (a directory name)
top directory into which the files will be unpacked
flag: -targ %s
scan_only: (an existing file name)
only scan the directory and put result in file
flag: -scanonly %s
spm_zeropad: (an integer (int or long))
set frame number zero padding width for SPM
flag: -nspmzeropad %d
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:
None