From a3beac4de9c5a742e754cb9af73762e1fb4428d5 Mon Sep 17 00:00:00 2001
From: Bogdan Petre <f0042vm@s06.hpcc.dartmouth.edu>
Date: Tue, 29 Oct 2024 18:27:15 -0400
Subject: [PATCH] Updated to keep in sync with image_vector/outliers.m

---
 .../__pycache__/preproc.cpython-39.pyc        | Bin 4750 -> 5121 bytes
 nipype/canlabCore/preproc.py                  |  12 ++++++++++--
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/nipype/canlabCore/__pycache__/preproc.cpython-39.pyc b/nipype/canlabCore/__pycache__/preproc.cpython-39.pyc
index 33c90fb815b0e543c793abfbfd73809487204322..d8b11a319e776f8fade4d68ded6be7fa71195d3a 100644
GIT binary patch
delta 1130
zcmaJ=&5ImG6z}S;>FMdOosnJ4cWT{TW+%IB6iv_sBt%^$NI<eV*qSt*sp^?p`eRbv
zlO=J67?PW;veZA2Tm+9{JtY5#hX(QDMZ|N!1mdgSm@mO<`d9UP^<KSK@4fnd>DICz
zd7iDoczAh!kj(D*htRh>D<{sSc3>loY7{3<;K1BS+|&y^q<yMUlQ!>Yw8<K`jlc(P
z(H8I)Gl0(kx2Xf%VHkLO=f^K+jS7Fxi?YIJ^E{~<>q#D!(nVcF<$LI}dC;eby42b>
z0*4vY1LoJvr85__UVHZkw1|)|f7VakoP%J65AerR7&q>03<WEOc|r-#NScy37lg8s
ziIitN8<4FbD~C*wRxF~FZSjH;%8OAF^;ycYlJJ5I`Cv#`mXBd7bJAy7k&89*F^i*d
zQfssdR+1~%2~X#u0Sm9OewmBo`M69t6UAC8AL*x&C*L*FWzmAzs#Z+HvW~2>KrM`U
z!hX`kyb4~y-xuWr;{*A`IBYvWJ@|`7xq#;_6PrkXDjd0vzgTxce!kZb`(PIP6&z4t
zDj*7;AGo)AOUV`hj=*2&02UGpyT9V^OxptXkrHo6;Vc9bZ4+%aDcUxtdTCMpHoDuI
z==adnDD8<s4T`t*DW2fF&OL3~m^3zBs6^v@&lCsY5OGMsVFk*SII4gEL|b_GcPG;4
zzPc8PNDO$kO1|mFw7VM9=_Pq}hRDn(9Uha#=P4o|lDFl3>rHvab>z0&T6)d)Sth%y
zFWKy!wVU}D(Q&WBl=sWZ<k@Ik7XKfhu;pJfD_<XjSSv)u63hWkljuriLL))FU&^UU
zXXS@toP|7tmWrWiJ^@*w?yMmTng4!|&87}z!*lwdm`Ks?BO-rkFTdXfy*e*FU97;m
zYC<>ELB6P5?Zpcdcp>4l-K+9s=h)3xt6nw3kmmg`6slt?yS{8#j99;}c;)Qb?n%~^
z-xCU6_^DTQhb+Q|S`_N(TL>S;2<z6WQ1V_U*q8Cq^%0Z5b%K+so5ec-m06Sm9+Xfv
ZbqKZF+U7q_<mMX(>{&>VYqUFU{10+T7OVgO

delta 831
zcmZ`$O=}ZD7~Ywk-E8(FO%t)PHf^GnB#j6Pf*%L*gX%#mMJRMHYs_rQ%I1UF%|T2M
zsW*)f=B6Mmcu?_{f8bH{CI|z9zrdRp5%isnSVi1npZ9&9nR!3vy<dHNB-3ylQ-SZb
zR@!=#8)p{KU|c`BiWI6)5}K|FRtv4R?b=AWtWce%9w;>BYul>p05@nFc-mKiXMmg3
z0&e*P_{{j#rh^5!8bq-m7rNb$&!Gz1;OEelyh<&Ks7;NL3Q3$BN-Z;aftC?+_<MXN
zy$@<)4gi0uo<$b_sJ08j==Ni;6@>mvg)Pbh629H!Avw*Tkg6#=k$0j+{*II}Gx=At
zzG{K8R@2yiuxw63L4q!!DB*XgskbDx62LtC5e6_2D@`704|OvI?4p#{c-cODouZL8
z#Bqw^ZM0(y@GcsvaeAOqm68!2k^$K<ca@<w&~97Mp(e{X0N0re%??UfkRZ!wyj3U9
z>;^XOR$8=jv_<*4Q<{93*+46{AT(&kLJvB<ejNQb1WWVH*}7YSXaZ4o2&_xmVdIw2
znIHAT_>Wd)mm=e_e#Z+svCmqKrhgu^NEW0Z1L@QCUDq+fKS&OLAw~Xqwuy@TQm%Sx
z8BQg2*D$MsFH$g^q`JN5OmaA02=n)T?FRgLZsp$JqYx?2qur+GF*!hCCS7__&u=DU
z5Z3hWRH@6nCnW6UNxWoiW!R7`l93EVmIxx)s4}V7vTmUh^zQV0el71FKL(P}qnHJq
cEtUq7WKS|C$N!1XKjr7mEWC`ZW}Phg3Hz9^<p2Nx

diff --git a/nipype/canlabCore/preproc.py b/nipype/canlabCore/preproc.py
index 66eec166..1aaff23d 100644
--- a/nipype/canlabCore/preproc.py
+++ b/nipype/canlabCore/preproc.py
@@ -5,7 +5,7 @@
     BaseInterfaceInputSpec,
     File,
 )
-from traits.api import List, Bool
+from traits.api import List, Bool, Float
 import os
 from string import Template
 
@@ -19,6 +19,10 @@ class OutliersInputSpec(BaseInterfaceInputSpec):
         desc="Indices of movement_file corresponding to rot_x, rot_y, rot_z, trans_x, trans_y, trans_z, in that order")
     movement_radians = Bool(default_value=True, usedefault=True, 
         desc="Are rotations specified in radians?")
+    fd_thresh = Float(-1, usedefault=True,
+        desc="Threshold in mm for determining whether \
+	framewise displacement is high enough to censor. Default is \
+	set by image_vector/outliers.m")
     out_file = File('outliers.csv', usedefault=True,
         desc="File indicate indices of volume to censor")
 
@@ -67,6 +71,7 @@ def _run_interface(self, runtime):
                  movement_file=self.inputs.movement_file,
                  movement_order=self.inputs.movement_order,
                  movement_radians=self.inputs.movement_radians,
+                 fd_thresh=self.inputs.fd_thresh,
                  out_file=self.inputs.out_file)
         # This is your MATLAB code template
         script = Template(
@@ -80,7 +85,10 @@ def _run_interface(self, runtime):
                                  if strcmp('$movement_radians','False')
                                      fd(:,1:3) = pi/180*fd(:,1:3);
                                  end
-                                 varargin={'fd',fd};
+                                 varargin=[varargin, {'fd',fd}];
+                             end
+                             if $fd_thresh > 0
+                                 varargin=[varargin, {'fd_thresh', $fd_thresh}];
                              end
                              [~,~,outlier_tables] = outliers(fmri_data(in_file), varargin{:});
                              outlier_ind = find(any(outlier_tables.outlier_regressor_matrix_corr,2))