Wraps command mri_binarize
Use FreeSurfer mri_binarize to threshold an input volume
>>> binvol = Binarize(in_file='structural.nii', min=10, binary_file='foo_out.nii')
>>> binvol.cmdline
'mri_binarize --o foo_out.nii --i structural.nii --min 10.000000'
Inputs:
[Mandatory]
in_file : (an existing file name)
input volume
[Optional]
abs : (a boolean)
take abs of invol first (ie, make unsigned)
args : (a string)
Additional parameters to the command
bin_col_num : (a boolean)
set binarized voxel value to its column number
bin_val : (an integer)
set vox within thresh to val (default is 1)
bin_val_not : (an integer)
set vox outside range to val (default is 0)
binary_file : (a file name)
binary output volume
count_file : (a boolean or a file name)
save number of hits in ascii file (hits,ntotvox,pct)
dilate : (an integer)
niters: dilate binarization in 3D
environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
Environment variables
erode : (an integer)
nerode: erode binarization in 3D (after any dilation)
erode2d : (an integer)
nerode2d: erode binarization in 2D (after any 3D erosion)
frame_no : (an integer)
use 0-based frame of input (default is 0)
invert : (a boolean)
set binval=0, binvalnot=1
mask_file : (an existing file name)
must be within mask
mask_thresh : (a float)
set thresh for mask
match : (a list of items which are an integer)
match instead of threshold
max : (a float)
max thresh
merge_file : (an existing file name)
merge with mergevol
min : (a float)
min thresh
out_type : ('nii' or 'nii.gz' or 'mgz')
output file type
rmax : (a float)
compute max based on rmax*globalmean
rmin : (a float)
compute min based on rmin*globalmean
subjects_dir : (an existing directory name)
subjects directory
ventricles : (a boolean)
set match vals those for aseg ventricles+choroid (not 4th)
wm : (a boolean)
set match vals to 2 and 41 (aseg for cerebral WM)
wm_ven_csf : (a boolean)
WM and ventricular CSF, including choroid (not 4th)
zero_edges : (a boolean)
zero the edge voxels
zero_slice_edge : (a boolean)
zero the edge slice voxels
Outputs:
binary_file : (an existing file name)
binarized output volume
count_file : (a file name)
ascii file containing number of hits
Wraps command mri_concat
Use Freesurfer mri_concat to combine several input volumes into one output volume. Can concatenate by frames, or compute a variety of statistics on the input volumes.
Combine two input volumes into one volume with two frames
>>> concat = Concatenate()
>>> concat.inputs.in_files = ['cont1.nii','cont2.nii']
>>> concat.inputs.concatenated_file = 'bar.nii'
>>> concat.cmdline
'mri_concat --o bar.nii --i cont1.nii --i cont2.nii'
Inputs:
[Mandatory]
in_files : (an existing file name)
Individual volumes to be concatenated
[Optional]
add_val : (a float)
Add some amount to the input volume
args : (a string)
Additional parameters to the command
combine : (a boolean)
Combine non-zero values into single frame volume
concatenated_file : (a file name)
Output volume
environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
Environment variables
gmean : (an integer)
create matrix to average Ng groups, Nper=Ntot/Ng
keep_dtype : (a boolean)
Keep voxelwise precision type (default is float
mask_file : (an existing file name)
Mask input with a volume
max_bonfcor : (a boolean)
Compute max and bonferroni correct (assumes -log10(ps))
max_index : (a boolean)
Compute the index of max voxel in concatenated volumes
mean_div_n : (a boolean)
compute mean/nframes (good for var)
multiply_by : (a float)
Multiply input volume by some amount
multiply_matrix_file : (an existing file name)
Multiply input by an ascii matrix in file
paired_stats : ('sum' or 'avg' or 'diff' or 'diff-norm' or 'diff-norm1' or 'diff-norm2')
Compute paired sum, avg, or diff
sign : ('abs' or 'pos' or 'neg')
Take only pos or neg voxles from input, or take abs
sort : (a boolean)
Sort each voxel by ascending frame value
stats : ('sum' or 'var' or 'std' or 'max' or 'min' or 'mean')
Compute the sum, var, std, max, min or mean of the input volumes
subjects_dir : (an existing directory name)
subjects directory
vote : (a boolean)
Most frequent value at each voxel and fraction of occurances
Outputs:
concatenated_file : (an existing file name)
Path/name of the output volume
Wraps command mri_glmfit
Use FreeSurfer mri_glmfit to prepare a group of contrasts for a second level analysis
>>> glmfit = GLMFit()
>>> glmfit.inputs.in_file = 'functional.nii'
>>> glmfit.inputs.one_sample = True
>>> glmfit.cmdline == 'mri_glmfit --glmdir %s --y functional.nii --osgm'%os.getcwd()
True
Inputs:
[Mandatory]
in_file : (a file name)
input 4D file
[Optional]
allow_ill_cond : (a boolean)
allow ill-conditioned design matrices
allow_repeated_subjects : (a boolean)
allow subject names to repeat in the fsgd file (must appear before --fsgd
args : (a string)
Additional parameters to the command
calc_AR1 : (a boolean)
compute and save temporal AR1 of residual
check_opts : (a boolean)
don't run anything, just check options and exit
compute_log_y : (a boolean)
compute natural log of y prior to analysis
contrast : (an existing file name)
contrast file
cortex : (a boolean)
use subjects ?h.cortex.label as label
exclusive: label_file
debug : (a boolean)
turn on debugging
design : (an existing file name)
design matrix file
exclusive: fsgd,design,one_sample
diag : (an integer)
Gdiag_no : set diagnositc level
diag_cluster : (a boolean)
save sig volume and exit from first sim loop
environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
Environment variables
fixed_fx_dof : (an integer)
dof for fixed effects analysis
exclusive: fixed_fx_dof_file
fixed_fx_dof_file : (a file name)
text file with dof for fixed effects analysis
exclusive: fixed_fx_dof
fixed_fx_var : (an existing file name)
for fixed effects analysis
force_perm : (a boolean)
force perumtation test, even when design matrix is not orthog
fsgd : (a tuple of the form: (an existing file name, 'doss' or 'dods'))
freesurfer descriptor file
exclusive: fsgd,design,one_sample
fwhm : (a float)
smooth input by fwhm
glm_dir : (a string)
save outputs to dir
invert_mask : (a boolean)
invert mask
label_file : (an existing file name)
use label as mask, surfaces only
exclusive: cortex
mask_file : (an existing file name)
binary mask
no_contrast_sok : (a boolean)
do not fail if no contrasts specified
no_est_fwhm : (a boolean)
turn off FWHM output estimation
no_mask_smooth : (a boolean)
do not mask when smoothing
no_prune : (a boolean)
do not prune
exclusive: prunethresh
one_sample : (a boolean)
construct X and C as a one-sample group mean
exclusive: one_sample,fsgd,design,contrast
pca : (a boolean)
perform pca/svd analysis on residual
per_voxel_reg : (an existing file name)
per-voxel regressors
profile : (an integer)
niters : test speed
prune : (a boolean)
remove voxels that do not have a non-zero value at each frame (def)
prune_thresh : (a float)
prune threshold. Default is FLT_MIN
exclusive: noprune
resynth_test : (an integer)
test GLM by resynthsis
save_cond : (a boolean)
flag to save design matrix condition at each voxel
save_estimate : (a boolean)
save signal estimate (yhat)
save_res_corr_mtx : (a boolean)
save residual error spatial correlation matrix (eres.scm). Big!
save_residual : (a boolean)
save residual error (eres)
seed : (an integer)
used for synthesizing noise
self_reg : (a tuple of the form: (an integer, an integer, an integer))
self-regressor from index col row slice
sim_done_file : (a file name)
create file when simulation finished
sim_sign : ('abs' or 'pos' or 'neg')
abs, pos, or neg
simulation : (a tuple of the form: ('perm' or 'mc-full' or 'mc-z', an integer, a float, a string))
nulltype nsim thresh csdbasename
subjects_dir : (an existing directory name)
subjects directory
surf : (a tuple of the form: (a string, 'lh' or 'rh', 'white' or 'pial' or 'smoothwm' or 'inflated'))
needed for some flags (uses white by default)
synth : (a boolean)
replace input with gaussian
uniform : (a tuple of the form: (a float, a float))
use uniform distribution instead of gaussian
var_fwhm : (a float)
smooth variance by fwhm
vox_dump : (a tuple of the form: (an integer, an integer, an integer))
dump voxel GLM and exit
weight_file : (an existing file name)
weight for each input at each voxel
exclusive: weighted_ls
weight_inv : (a boolean)
invert weights
exclusive: weighted_ls
weight_sqrt : (a boolean)
sqrt of weights
exclusive: weighted_ls
weighted_ls : (an existing file name)
weighted least squares
exclusive: weight_file,weight_inv,weight_sqrt
Wraps command mri_label2vol
Make a binary volume from a Freesurfer label
>>> binvol = Label2Vol(label_file='cortex.label', template_file='structural.nii', reg_file='register.dat', fill_thresh=0.5, vol_label_file='foo_out.nii')
>>> binvol.cmdline
'mri_label2vol --fillthresh 0 --label cortex.label --reg register.dat --temp structural.nii --o foo_out.nii'
Inputs:
[Mandatory]
annot_file : (an existing file name)
surface annotation file
exclusive: label_file,annot_file,seg_file,aparc_aseg
requires: subjectid,hemi
aparc_aseg : (a boolean)
use aparc+aseg.mgz in subjectdir as seg
exclusive: label_file,annot_file,seg_file,aparc_aseg
label_file : (an existing file name)
list of label files
exclusive: label_file,annot_file,seg_file,aparc_aseg
seg_file : (an existing file name)
segmentation file
exclusive: label_file,annot_file,seg_file,aparc_aseg
template_file : (an existing file name)
output template volume
[Optional]
args : (a string)
Additional parameters to the command
environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
Environment variables
fill_thresh : (0.0 <= a floating point number <= 1.0)
thresh : between 0 and 1
hemi : ('lh' or 'rh')
hemisphere to use lh or rh
identity : (a boolean)
set R=I
exclusive: reg_file,reg_header,identity
invert_mtx : (a boolean)
Invert the registration matrix
label_hit_file : (a file name)
file with each frame is nhits for a label
label_voxel_volume : (a float)
volume of each label point (def 1mm3)
map_label_stat : (a file name)
map the label stats field into the vol
native_vox2ras : (a boolean)
use native vox2ras xform instead of tkregister-style
proj : (a tuple of the form: ('abs' or 'frac', a float, a float, a float))
project along surface normal
reg_file : (an existing file name)
tkregister style matrix VolXYZ = R*LabelXYZ
exclusive: reg_file,reg_header,identity
reg_header : (an existing file name)
label template volume
exclusive: reg_file,reg_header,identity
subject_id : (a string)
subject id
subjects_dir : (an existing directory name)
subjects directory
surface : (a string)
use surface instead of white
vol_label_file : (a file name)
output volume
Outputs:
vol_label_file : (an existing file name)
output volume
Wraps command mris_preproc
Use FreeSurfer mris_preproc to prepare a group of contrasts for a second level analysis
>>> preproc = MRISPreproc()
>>> preproc.inputs.target = 'fsaverage'
>>> preproc.inputs.hemi = 'lh'
>>> preproc.inputs.vol_measure_file = [('cont1.nii', 'register.dat'), ('cont1a.nii', 'register.dat')]
>>> preproc.inputs.out_file = 'concatenated_file.mgz'
>>> preproc.cmdline
'mris_preproc --hemi lh --out concatenated_file.mgz --target fsaverage --iv cont1.nii register.dat --iv cont1a.nii register.dat'
Inputs:
[Mandatory]
hemi : ('lh' or 'rh')
hemisphere for source and target
target : (a string)
target subject name
[Optional]
args : (a string)
Additional parameters to the command
environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
Environment variables
fsgd_file : (an existing file name)
specify subjects using fsgd file
exclusive: subjects,fsgd_file,subject_file
fwhm : (a float)
smooth by fwhm mm on the target surface
exclusive: num_iters
fwhm_source : (a float)
smooth by fwhm mm on the source surface
exclusive: num_iters_source
num_iters : (an integer)
niters : smooth by niters on the target surface
exclusive: fwhm
num_iters_source : (an integer)
niters : smooth by niters on the source surface
exclusive: fwhm_source
out_file : (a file name)
output filename
proj_frac : (a float)
projection fraction for vol2surf
smooth_cortex_only : (a boolean)
only smooth cortex (ie, exclude medial wall)
source_format : (a string)
source format
subject_file : (an existing file name)
file specifying subjects separated by white space
exclusive: subjects,fsgd_file,subject_file
subjects : (a list of items which are any value)
subjects from who measures are calculated
exclusive: subjects,fsgd_file,subject_file
subjects_dir : (an existing directory name)
subjects directory
surf_area : (a string)
Extract vertex area from subject/surf/hemi.surfname to use as input.
exclusive: surf_measure,surf_measure_file,surf_area
surf_dir : (a string)
alternative directory (instead of surf)
surf_measure : (a string)
Use subject/surf/hemi.surf_measure as input
exclusive: surf_measure,surf_measure_file,surf_area
surf_measure_file : (an existing file name)
file alternative to surfmeas, still requires list of subjects
exclusive: surf_measure,surf_measure_file,surf_area
vol_measure_file : (a tuple of the form: (an existing file name, an existing file name))
list of volume measure and reg file tuples
Outputs:
out_file : (an existing file name)
preprocessed output file
Wraps command mri_glmfit
Inputs:
[Mandatory]
in_file : (a file name)
input 4D file
[Optional]
allow_ill_cond : (a boolean)
allow ill-conditioned design matrices
allow_repeated_subjects : (a boolean)
allow subject names to repeat in the fsgd file (must appear before --fsgd
args : (a string)
Additional parameters to the command
calc_AR1 : (a boolean)
compute and save temporal AR1 of residual
check_opts : (a boolean)
don't run anything, just check options and exit
compute_log_y : (a boolean)
compute natural log of y prior to analysis
contrast : (an existing file name)
contrast file
cortex : (a boolean)
use subjects ?h.cortex.label as label
exclusive: label_file
debug : (a boolean)
turn on debugging
design : (an existing file name)
design matrix file
exclusive: fsgd,design,one_sample
diag : (an integer)
Gdiag_no : set diagnositc level
diag_cluster : (a boolean)
save sig volume and exit from first sim loop
environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
Environment variables
fixed_fx_dof : (an integer)
dof for fixed effects analysis
exclusive: fixed_fx_dof_file
fixed_fx_dof_file : (a file name)
text file with dof for fixed effects analysis
exclusive: fixed_fx_dof
fixed_fx_var : (an existing file name)
for fixed effects analysis
force_perm : (a boolean)
force perumtation test, even when design matrix is not orthog
fsgd : (a tuple of the form: (an existing file name, 'doss' or 'dods'))
freesurfer descriptor file
exclusive: fsgd,design,one_sample
fwhm : (a float)
smooth input by fwhm
glm_dir : (a string)
save outputs to dir
invert_mask : (a boolean)
invert mask
label_file : (an existing file name)
use label as mask, surfaces only
exclusive: cortex
mask_file : (an existing file name)
binary mask
no_contrast_sok : (a boolean)
do not fail if no contrasts specified
no_est_fwhm : (a boolean)
turn off FWHM output estimation
no_mask_smooth : (a boolean)
do not mask when smoothing
no_prune : (a boolean)
do not prune
exclusive: prunethresh
one_sample : (a boolean)
construct X and C as a one-sample group mean
exclusive: one_sample,fsgd,design,contrast
pca : (a boolean)
perform pca/svd analysis on residual
per_voxel_reg : (an existing file name)
per-voxel regressors
profile : (an integer)
niters : test speed
prune : (a boolean)
remove voxels that do not have a non-zero value at each frame (def)
prune_thresh : (a float)
prune threshold. Default is FLT_MIN
exclusive: noprune
resynth_test : (an integer)
test GLM by resynthsis
save_cond : (a boolean)
flag to save design matrix condition at each voxel
save_estimate : (a boolean)
save signal estimate (yhat)
save_res_corr_mtx : (a boolean)
save residual error spatial correlation matrix (eres.scm). Big!
save_residual : (a boolean)
save residual error (eres)
seed : (an integer)
used for synthesizing noise
self_reg : (a tuple of the form: (an integer, an integer, an integer))
self-regressor from index col row slice
sim_done_file : (a file name)
create file when simulation finished
sim_sign : ('abs' or 'pos' or 'neg')
abs, pos, or neg
simulation : (a tuple of the form: ('perm' or 'mc-full' or 'mc-z', an integer, a float, a string))
nulltype nsim thresh csdbasename
subjects_dir : (an existing directory name)
subjects directory
surf : (a tuple of the form: (a string, 'lh' or 'rh', 'white' or 'pial' or 'smoothwm' or 'inflated'))
needed for some flags (uses white by default)
synth : (a boolean)
replace input with gaussian
uniform : (a tuple of the form: (a float, a float))
use uniform distribution instead of gaussian
var_fwhm : (a float)
smooth variance by fwhm
vox_dump : (a tuple of the form: (an integer, an integer, an integer))
dump voxel GLM and exit
weight_file : (an existing file name)
weight for each input at each voxel
exclusive: weighted_ls
weight_inv : (a boolean)
invert weights
exclusive: weighted_ls
weight_sqrt : (a boolean)
sqrt of weights
exclusive: weighted_ls
weighted_ls : (an existing file name)
weighted least squares
exclusive: weight_file,weight_inv,weight_sqrt
Wraps command mri_segstats
Use FreeSurfer mri_segstats for ROI analysis
>>> import nipype.interfaces.freesurfer as fs
>>> ss = fs.SegStats()
>>> ss.inputs.annot = ('PWS04', 'lh', 'aparc')
>>> ss.inputs.in_file = 'functional.nii'
>>> ss.inputs.subjects_dir = '.'
>>> ss.inputs.avgwf_txt_file = './avgwf.txt'
>>> ss.inputs.summary_file = './summary.stats'
>>> ss.cmdline
'mri_segstats --annot PWS04 lh aparc --avgwf ./avgwf.txt --i functional.nii --sum ./summary.stats'
Inputs:
[Mandatory]
annot : (a tuple of the form: (a string, 'lh' or 'rh', a string))
subject hemi parc : use surface parcellation
exclusive: segmentation_file,annot,surf_label
segmentation_file : (an existing file name)
segmentation volume path
exclusive: segmentation_file,annot,surf_label
surf_label : (a tuple of the form: (a string, 'lh' or 'rh', a string))
subject hemi label : use surface label
exclusive: segmentation_file,annot,surf_label
[Optional]
args : (a string)
Additional parameters to the command
avgwf_file : (a boolean or a file name)
Save as binary volume (bool or filename)
avgwf_txt_file : (a boolean or a file name)
Save average waveform into file (bool or filename)
brain_vol : ('brain-vol-from-seg' or 'brainmask' or '--%s')
Compute brain volume either with ``brainmask`` or ``brain-vol-from-seg``
calc_power : ('sqr' or 'sqrt')
Compute either the sqr or the sqrt of the input
calc_snr : (a boolean)
save mean/std as extra column in output table
color_table_file : (an existing file name)
color table file with seg id names
exclusive: color_table_file,default_color_table,gca_color_table
cortex_vol_from_surf : (a boolean)
Compute cortex volume from surf
default_color_table : (a boolean)
use $FREESURFER_HOME/FreeSurferColorLUT.txt
exclusive: color_table_file,default_color_table,gca_color_table
environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
Environment variables
etiv : (a boolean)
Compute ICV from talairach transform
etiv_only : ('etiv' or 'old-etiv' or '--%s-only')
Compute etiv and exit. Use ``etiv`` or ``old-etiv``
exclude_ctx_gm_wm : (a boolean)
exclude cortical gray and white matter
exclude_id : (an integer)
Exclude seg id from report
frame : (an integer)
Report stats on nth frame of input volume
gca_color_table : (an existing file name)
get color table from GCA (CMA)
exclusive: color_table_file,default_color_table,gca_color_table
in_file : (an existing file name)
Use the segmentation to report stats on this volume
mask_erode : (an integer)
Erode mask by some amount
mask_file : (an existing file name)
Mask volume (same size as seg
mask_frame : (an integer)
Mask with this (0 based) frame of the mask volume
requires: mask_file
mask_invert : (a boolean)
Invert binarized mask volume
mask_sign : ('abs' or 'pos' or 'neg' or '--masksign %s')
Sign for mask threshold: pos, neg, or abs
mask_thresh : (a float)
binarize mask with this threshold <0.5>
multiply : (a float)
multiply input by val
non_empty_only : (a boolean)
Only report nonempty segmentations
partial_volume_file : (an existing file name)
Compensate for partial voluming
segment_id : (a list of items which are any value)
Manually specify segmentation ids
sf_avg_file : (a boolean or a file name)
Save mean across space and time
subjects_dir : (an existing directory name)
subjects directory
summary_file : (a file name)
Segmentation stats summary table file
vox : (a list of items which are an integer)
Replace seg with all 0s except at C R S (three int inputs)
wm_vol_from_surf : (a boolean)
Compute wm volume from surf
Outputs:
avgwf_file : (a file name)
Volume with functional statistics averaged over segs
avgwf_txt_file : (a file name)
Text file with functional statistics averaged over segs
sf_avg_file : (a file name)
Text file with func statistics averaged over segs and framss
summary_file : (an existing file name)
Segmentation summary statistics table