Merge pull request #323 from a3sha2/master

a3sha2 · web-flow · commit 6bd62f64d8e9 · 2020-04-10T00:33:05.000-04:00
cifiti outputs and  documentation
diff --git a/core/VERSION b/core/VERSION
@@ -1 +1 @@
-xcpEngine-v1.0
+xcpEngine-v1.1
diff --git a/docs/modules/regress.rst b/docs/modules/regress.rst
@@ -247,3 +247,6 @@ The optional output is the spatially smoothed residualised BOLD signal. This is
 This tells xcpEngine to smooth the residualised image with gaussian filter and kernel of 6mm. The derived
 output, which is saved in the ``regress`` folder, will be::
   prefix_img_sm6.nii.gz
+
+If the freesurfer is included as part of FMRIPREP outputs, the CIFTI files are produced 
+for filtered  and  regressed bold data (`${prefix}_residualised.nii.gz`) 
diff --git a/docs/modules/task.rst b/docs/modules/task.rst
@@ -65,3 +65,6 @@ The  outputs also consist of Quality Assesmment between structrual and BOLD imag
     - ``prefix_coregCrossCorr.txt`` : Cross correlation
     - ``prefix_coregDice.txt`` : Dice index
     - ``prefix_coregJaccard.txt`` : Jaccard index 
+
+If the freesurfer is included as part of FMRIPREP outputs, the CIFTI files are produced 
+for task and confound regressed bold data (`res4d.nii.gz`)  
diff --git a/xcpEngine b/xcpEngine
@@ -19,6 +19,13 @@ args=`echo $@`
  Development team:
  Lead:         Rastko Ciric
                rastko@mail.med.upenn.edu
+
+ Maintainers and contributors:
+           Azeez Adebimpe 
+           adebimpe@upenn.edu
+           Matt Cieslak 
+           mcieslak@upenn.edu
+
  Multimodal:   Adon FG Rosen
                adrose@mail.med.upenn.edu
  PI:           Ted Satterthwaite
@@ -34,12 +41,10 @@ args=`echo $@`
  As a courtesy, we ask that you include the following citations
  in publications that make use of this program:
 
- Ciric R, Wolf DH, Power JD, Roalf DR, Baum GL, Ruparel K,
-    Shinohara RT, Elliott MA, Eickhoff SB, Davatzikos C, Gur RC,
-    Gur RE, Bassett DS, Satterthwaite TD (in press)
-    Benchmarking participant-level confound regression strategies
-    for the control of motion artifact in studies of functional
-    connectivity. NeuroImage.
+ , Rastko Ciric, Adon F. G. Rosen, Guray Erus, Matthew Cieslak, Azeez Adebimpe, 
+ Philip A. Cook, Danielle S. Bassett, Christos Davatzikos, Daniel H. Wolf, 
+ Theodore D. Satterthwaite Mitigating head motion artifact in functional 
+ connectivity MRI,Nature Protocol 
 
  Dependencies:
   * FSL (available from FMRIB)
