smriprep.interfaces.freesurfer module
Nipype’s recon-all replacement.
- class smriprep.interfaces.freesurfer.MRIsConvertData(**inputs)[source]
Bases:
MRIsConvert
Wrapped executable:
mris_convert
.Convert surface data files (label, curvature, functional, etc) Wraps mris_convert to automatically select the correct ?h.white surface if passed a file from the subject’s surf/ directory
- Mandatory Inputs:
annot_file (a pathlike object or string representing an existing file) – Input is annotation or gifti label data. Maps to a command-line argument:
--annot %s
. Mutually exclusive with inputs:annot_file
,parcstats_file
,label_file
,scalarcurv_file
,functional_file
.functional_file (a pathlike object or string representing an existing file) – Input is functional time-series or other multi-frame data (must specify surface). Maps to a command-line argument:
-f %s
. Mutually exclusive with inputs:annot_file
,parcstats_file
,label_file
,scalarcurv_file
,functional_file
.label_file (a pathlike object or string representing an existing file) – Infile is .label file, label is name of this label. Maps to a command-line argument:
--label %s
. Mutually exclusive with inputs:annot_file
,parcstats_file
,label_file
,scalarcurv_file
,functional_file
.out_datatype (‘asc’ or ‘ico’ or ‘tri’ or ‘stl’ or ‘vtk’ or ‘gii’ or ‘mgh’ or ‘mgz’) – These file formats are supported: ASCII: .ascICO: .ico, .tri GEO: .geo STL: .stl VTK: .vtk GIFTI: .gii MGH surface-encoded ‘volume’: .mgh, .mgz. Mutually exclusive with inputs:
out_file
.out_file (a pathlike object or string representing a file) – Output filename or True to generate one. Maps to a command-line argument:
%s
(position: -1). Mutually exclusive with inputs:out_datatype
.parcstats_file (a pathlike object or string representing an existing file) – Infile is name of text file containing label/val pairs. Maps to a command-line argument:
--parcstats %s
. Mutually exclusive with inputs:annot_file
,parcstats_file
,label_file
,scalarcurv_file
,functional_file
.scalarcurv_file (a pathlike object or string representing an existing file) – Input is scalar curv overlay file (must still specify surface). Maps to a command-line argument:
-c %s
. Mutually exclusive with inputs:annot_file
,parcstats_file
,label_file
,scalarcurv_file
,functional_file
.
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.dataarray_num (an integer) – If input is gifti, ‘num’ specifies which data array to use. Maps to a command-line argument:
--da_num %d
.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)in_file (a pathlike object or string representing an existing file) – Surface file. Maps to a command-line argument:
%s
(position: -2).labelstats_outfile (a pathlike object or string representing a file) – Outfile is name of gifti file to which label stats will be written. Maps to a command-line argument:
--labelstats %s
.normal (a boolean) – Output is an ascii file where vertex data. Maps to a command-line argument:
-n
.origname (a string) – Read orig positions. Maps to a command-line argument:
-o %s
.patch (a boolean) – Input is a patch, not a full surface. Maps to a command-line argument:
-p
.rescale (a boolean) – Rescale vertex xyz so total area is same as group average. Maps to a command-line argument:
-r
.scale (a float) – Scale vertex xyz by scale. Maps to a command-line argument:
-s %.3f
.subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.
talairachxfm_subjid (a string) – Apply talairach xfm of subject to vertex xyz. Maps to a command-line argument:
-t %s
.to_scanner (a boolean) – Convert coordinates from native FS (tkr) coords to scanner coords. Maps to a command-line argument:
--to-scanner
.to_tkr (a boolean) – Convert coordinates from scanner coords to native FS (tkr) coords. Maps to a command-line argument:
--to-tkr
.vertex (a boolean) – Writes out neighbors of a vertex in each row. Maps to a command-line argument:
-v
.xyz_ascii (a boolean) – Print only surface xyz to ascii file. Maps to a command-line argument:
-a
.
- Outputs:
converted (a pathlike object or string representing an existing file) – Converted output surface.
- class smriprep.interfaces.freesurfer.MakeMidthickness(**inputs)[source]
Bases:
MakeMidthickness
,FSCommandOpenMP
Wrapped executable:
mris_expand
.Patched MakeMidthickness interface
Ensures output filenames are specified with hemisphere labels, when appropriate. This may not cover all use-cases in MRIsExpand, but we’re just making midthickness files.
This interface also sets the OMP_NUM_THREADS environment variable to floor(1.5x) the number of threads requested by the user, as tests indicate that cores are underutilized by a factor of 2/3.
>>> from smriprep.interfaces.freesurfer import MakeMidthickness >>> mris_expand = MakeMidthickness(thickness=True, distance=0.5) >>> mris_expand.inputs.in_file = 'lh.white' >>> mris_expand.cmdline 'mris_expand -thickness lh.white 0.5 lh.expanded' >>> mris_expand.inputs.out_name = 'graymid' >>> mris_expand.cmdline 'mris_expand -thickness lh.white 0.5 lh.graymid'
Explicit hemisphere labels should still be respected:
>>> mris_expand.inputs.out_name = 'rh.graymid' >>> mris_expand.cmdline 'mris_expand -thickness lh.white 0.5 rh.graymid'
- Mandatory Inputs:
distance (a float) – Distance in mm or fraction of cortical thickness. Maps to a command-line argument:
%g
(position: -2).in_file (a pathlike object or string representing an existing file) – Surface to expand. Maps to a command-line argument:
%s
(position: -3).
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.dt (a float) – Dt (implicit: 0.25). Maps to a command-line argument:
-T %g
.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)graymid (a list of items which are any value) – Existing graymid/midthickness file.
nsurfaces (an integer) – Number of surfacces to write during expansion. Maps to a command-line argument:
-N %d
.num_threads (an integer) – Allows for specifying more threads.
out_name (a string) – Output surface file. If no path, uses directory of
in_file
. If no path AND missing “lh.” or “rh.”, derive fromin_file
. Maps to a command-line argument:%s
(position: -1). (Nipype default value:expanded
)pial (a string) – Name of pial file (implicit: “pial”) If no path, uses directory of
in_file
If no path AND missing “lh.” or “rh.”, derive fromin_file
. Maps to a command-line argument:-pial %s
.smooth_averages (an integer) – Smooth surface with N iterations after expansion. Maps to a command-line argument:
-A %d
.sphere (a string) – WARNING: Do not change this trait. (Nipype default value:
sphere
)spring (a float) – Spring term (implicit: 0.05). Maps to a command-line argument:
-S %g
.subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.
thickness (a boolean) – Expand by fraction of cortical thickness, not mm. Maps to a command-line argument:
-thickness
.thickness_name (a string) – Name of thickness file (implicit: “thickness”) If no path, uses directory of
in_file
If no path AND missing “lh.” or “rh.”, derive from in_file. Maps to a command-line argument:-thickness_name %s
.write_iterations (an integer) – Write snapshots of expansion every N iterations. Maps to a command-line argument:
-W %d
.
- Outputs:
out_file (a pathlike object or string representing a file) – Output surface file.
- class smriprep.interfaces.freesurfer.ReconAll(command=None, terminal_output=None, write_cmdline=False, **inputs)[source]
Bases:
ReconAll
Wrapped executable:
recon-all
.- Optional Inputs:
FLAIR_file (a pathlike object or string representing an existing file) – Convert FLAIR image to orig directory. Maps to a command-line argument:
-FLAIR %s
.T1_files (a list of items which are a pathlike object or string representing an existing file) – Name of T1 file to process. Maps to a command-line argument:
-i %s...
.T2_file (a pathlike object or string representing an existing file) – Convert T2 image to orig directory. Maps to a command-line argument:
-T2 %s
.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.big_ventricles (a boolean) – For use in subjects with enlarged ventricles. Maps to a command-line argument:
-bigventricles
.brainstem (a boolean) – Segment brainstem structures. Maps to a command-line argument:
-brainstem-structures
.directive (‘all’ or ‘autorecon1’ or ‘autorecon2’ or ‘autorecon2-volonly’ or ‘autorecon2-perhemi’ or ‘autorecon2-inflate1’ or ‘autorecon2-cp’ or ‘autorecon2-wm’ or ‘autorecon3’ or ‘autorecon3-T2pial’ or ‘autorecon-pial’ or ‘autorecon-hemi’ or ‘localGI’ or ‘qcache’) – Process directive. Maps to a command-line argument:
-%s
(position: 0). Mutually exclusive with inputs:steps
. (Nipype default value:all
)environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)expert (a pathlike object or string representing an existing file) – Set parameters using expert file. Maps to a command-line argument:
-expert %s
.flags (a list of items which are a string) – Additional parameters. Maps to a command-line argument:
%s
.hemi (‘lh’ or ‘rh’) – Hemisphere to process. Maps to a command-line argument:
-%s-only
.hippocampal_subfields_T1 (a boolean) – Segment hippocampal subfields using input T1 scan. Maps to a command-line argument:
-hippocampal-subfields-T1
.hippocampal_subfields_T2 (a tuple of the form: (a pathlike object or string representing an existing file, a string)) – Segment hippocampal subfields using T2 scan, identified by ID (may be combined with hippocampal_subfields_T1). Maps to a command-line argument:
-hippocampal-subfields-T2 %s %s
.hires (a boolean) – Conform to minimum voxel size (for voxels < 1mm). Maps to a command-line argument:
-hires
.mprage (a boolean) – Assume scan parameters are MGH MP-RAGE protocol, which produces darker gray matter. Maps to a command-line argument:
-mprage
.mri_aparc2aseg (a string) – Flags to pass to mri_aparc2aseg commands. Mutually exclusive with inputs:
expert
.mri_ca_label (a string) – Flags to pass to mri_ca_label commands. Mutually exclusive with inputs:
expert
.mri_ca_normalize (a string) – Flags to pass to mri_ca_normalize commands. Mutually exclusive with inputs:
expert
.mri_ca_register (a string) – Flags to pass to mri_ca_register commands. Mutually exclusive with inputs:
expert
.mri_edit_wm_with_aseg (a string) – Flags to pass to mri_edit_wm_with_aseg commands. Mutually exclusive with inputs:
expert
.mri_em_register (a string) – Flags to pass to mri_em_register commands. Mutually exclusive with inputs:
expert
.mri_fill (a string) – Flags to pass to mri_fill commands. Mutually exclusive with inputs:
expert
.mri_mask (a string) – Flags to pass to mri_mask commands. Mutually exclusive with inputs:
expert
.mri_normalize (a string) – Flags to pass to mri_normalize commands. Mutually exclusive with inputs:
expert
.mri_pretess (a string) – Flags to pass to mri_pretess commands. Mutually exclusive with inputs:
expert
.mri_remove_neck (a string) – Flags to pass to mri_remove_neck commands. Mutually exclusive with inputs:
expert
.mri_segment (a string) – Flags to pass to mri_segment commands. Mutually exclusive with inputs:
expert
.mri_segstats (a string) – Flags to pass to mri_segstats commands. Mutually exclusive with inputs:
expert
.mri_tessellate (a string) – Flags to pass to mri_tessellate commands. Mutually exclusive with inputs:
expert
.mri_watershed (a string) – Flags to pass to mri_watershed commands. Mutually exclusive with inputs:
expert
.mris_anatomical_stats (a string) – Flags to pass to mris_anatomical_stats commands. Mutually exclusive with inputs:
expert
.mris_ca_label (a string) – Flags to pass to mris_ca_label commands. Mutually exclusive with inputs:
expert
.mris_fix_topology (a string) – Flags to pass to mris_fix_topology commands. Mutually exclusive with inputs:
expert
.mris_inflate (a string) – Flags to pass to mri_inflate commands. Mutually exclusive with inputs:
expert
.mris_make_surfaces (a string) – Flags to pass to mris_make_surfaces commands. Mutually exclusive with inputs:
expert
.mris_register (a string) – Flags to pass to mris_register commands. Mutually exclusive with inputs:
expert
.mris_smooth (a string) – Flags to pass to mri_smooth commands. Mutually exclusive with inputs:
expert
.mris_sphere (a string) – Flags to pass to mris_sphere commands. Mutually exclusive with inputs:
expert
.mris_surf2vol (a string) – Flags to pass to mris_surf2vol commands. Mutually exclusive with inputs:
expert
.mrisp_paint (a string) – Flags to pass to mrisp_paint commands. Mutually exclusive with inputs:
expert
.openmp (an integer) – Number of processors to use in parallel. Maps to a command-line argument:
-openmp %d
.parallel (a boolean) – Enable parallel execution. Maps to a command-line argument:
-parallel
.steps (a list of items which are ‘motioncor’ or ‘talairach’ or ‘nuintensitycor’ or ‘normalization’ or ‘skullstrip’ or ‘gcareg’ or ‘canorm’ or ‘careg’ or ‘careginv’ or ‘rmneck’ or ‘skull-lta’ or ‘calabel’ or ‘normalization2’ or ‘maskbfs’ or ‘segmentation’ or ‘tessellate’ or ‘smooth1’ or ‘inflate1’ or ‘qsphere’ or ‘fix’ or ‘white’ or ‘smooth2’ or ‘inflate2’ or ‘curvHK’ or ‘curvstats’ or ‘sphere’ or ‘surfreg’ or ‘jacobian_white’ or ‘avgcurv’ or ‘cortparc’ or ‘pial’ or ‘pctsurfcon’ or ‘parcstats’ or ‘cortparc2’ or ‘parcstats2’ or ‘cortparc3’ or ‘parcstats3’ or ‘label-exvivo-ec’ or ‘cortribbon’ or ‘hyporelabel’ or ‘segstats’ or ‘aparc2aseg’ or ‘apas2aseg’ or ‘wmparc’ or ‘balabels’) – Specific process directives. Mutually exclusive with inputs:
directive
.subject_id (a string) – Subject name. Maps to a command-line argument:
-subjid %s
. (Nipype default value:recon_all
)subjects_dir (a pathlike object or string representing an existing directory) – Path to subjects directory. Maps to a command-line argument:
-sd %s
.talairach (a string) – Flags to pass to talairach commands. Mutually exclusive with inputs:
expert
.use_FLAIR (a boolean) – Use FLAIR image to refine the pial surface. Maps to a command-line argument:
-FLAIRpial
. Mutually exclusive with inputs:use_T2
.use_T2 (a boolean) – Use T2 image to refine the pial surface. Maps to a command-line argument:
-T2pial
. Mutually exclusive with inputs:use_FLAIR
.xopts (‘use’ or ‘clean’ or ‘overwrite’) – Use, delete or overwrite existing expert options file. Maps to a command-line argument:
-xopts-%s
.
- Outputs:
BA_stats (a list of items which are a pathlike object or string representing an existing file) – Brodmann Area statistics files.
T1 (a pathlike object or string representing an existing file) – Intensity normalized whole-head volume.
annot (a list of items which are a pathlike object or string representing an existing file) – Surface annotation files.
aparc_a2009s_stats (a list of items which are a pathlike object or string representing an existing file) – Aparc a2009s parcellation statistics files.
aparc_aseg (a list of items which are a pathlike object or string representing an existing file) – Aparc parcellation projected into aseg volume.
aparc_stats (a list of items which are a pathlike object or string representing an existing file) – Aparc parcellation statistics files.
area_pial (a list of items which are a pathlike object or string representing an existing file) – Mean area of triangles each vertex on the pial surface is associated with.
aseg (a pathlike object or string representing an existing file) – Volumetric map of regions from automatic segmentation.
aseg_stats (a list of items which are a pathlike object or string representing an existing file) – Automated segmentation statistics file.
avg_curv (a list of items which are a pathlike object or string representing an existing file) – Average atlas curvature, sampled to subject.
brain (a pathlike object or string representing an existing file) – Intensity normalized brain-only volume.
brainmask (a pathlike object or string representing an existing file) – Skull-stripped (brain-only) volume.
curv (a list of items which are a pathlike object or string representing an existing file) – Maps of surface curvature.
curv_pial (a list of items which are a pathlike object or string representing an existing file) – Curvature of pial surface.
curv_stats (a list of items which are a pathlike object or string representing an existing file) – Curvature statistics files.
entorhinal_exvivo_stats (a list of items which are a pathlike object or string representing an existing file) – Entorhinal exvivo statistics files.
filled (a pathlike object or string representing an existing file) – Subcortical mass volume.
graymid (a list of items which are a pathlike object or string representing an existing file) – Graymid/midthickness surface meshes.
inflated (a list of items which are a pathlike object or string representing an existing file) – Inflated surface meshes.
jacobian_white (a list of items which are a pathlike object or string representing an existing file) – Distortion required to register to spherical atlas.
label (a list of items which are a pathlike object or string representing an existing file) – Volume and surface label files.
norm (a pathlike object or string representing an existing file) – Normalized skull-stripped volume.
nu (a pathlike object or string representing an existing file) – Non-uniformity corrected whole-head volume.
orig (a pathlike object or string representing an existing file) – Base image conformed to Freesurfer space.
pial (a list of items which are a pathlike object or string representing an existing file) – Gray matter/pia mater surface meshes.
rawavg (a pathlike object or string representing an existing file) – Volume formed by averaging input images.
ribbon (a list of items which are a pathlike object or string representing an existing file) – Volumetric maps of cortical ribbons.
smoothwm (a list of items which are a pathlike object or string representing an existing file) – Smoothed original surface meshes.
sphere (a list of items which are a pathlike object or string representing an existing file) – Spherical surface meshes.
sphere_reg (a list of items which are a pathlike object or string representing an existing file) – Spherical registration file.
subject_id (a string) – Subject name for whom to retrieve data.
subjects_dir (a pathlike object or string representing an existing directory) – Freesurfer subjects directory.
sulc (a list of items which are a pathlike object or string representing an existing file) – Surface maps of sulcal depth.
thickness (a list of items which are a pathlike object or string representing an existing file) – Surface maps of cortical thickness.
volume (a list of items which are a pathlike object or string representing an existing file) – Surface maps of cortical volume.
white (a list of items which are a pathlike object or string representing an existing file) – White/gray matter surface meshes.
wm (a pathlike object or string representing an existing file) – Segmented white-matter volume.
wmparc (a pathlike object or string representing an existing file) – Aparc parcellation projected into subcortical white matter.
wmparc_stats (a list of items which are a pathlike object or string representing an existing file) – White matter parcellation statistics file.
- property cmdline
command plus any arguments (args) validates arguments and generates command line