PennLINC · zhao-cy · Dec 15, 2023 · Dec 14, 2023 · Dec 14, 2023 · Dec 14, 2023
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,17 +1,17 @@
 Package: ModelArray
 Title: An R package for statistical analysis of fixel-wise data and beyond
-Version: 0.1.4
+Version: 0.1.4.9000
 Authors@R:
     c(person(given = "Chenying",
            family = "Zhao",
-           role = c("aut", "cre"),
-           email = "chenyzh@seas.upenn.edu"),
+           role = c("aut")),
        person(give = "Tinashe",
             family = "Tapera",
             role = c("aut")),
        person(give = "Matthew",
             family = "Cieslak",
-            role = c("aut")),
+            role = c("aut", "cre"),
+            email = "Matthew.Cieslak@pennmedicine.upenn.edu"),
         person(give = "Theodore",
             family = "Satterthwaite",
             role = c("aut")) )

diff --git a/README.Rmd b/README.Rmd
@@ -27,11 +27,11 @@ knitr::opts_chunk$set(
 * Supporting linear and nonlinear modeling, and extensible to more models: 
   * At present, `ModelArray` supports linear models as well as generalized additive models (GAMs) with and without penalized splines, which are particularly useful for studying nonlinear effects in lifespan data. `ModelArray` is also extensible to diverse models available in R;
 * Scalable for large-scale datasets;
-* Compatible with fixel-wise data and voxel-wise data.
+* Compatible with fixel-wise data, voxel-wise data, and greyordinate-wise data.
 
 Please cite our [NeuroImage paper](https://doi.org/10.1016/j.neuroimage.2023.120037) if you use `ModelArray`: 
 
-> Zhao, C., Tapera, T. M., Bagautdinova, J., Bourque, J., Covitz, S., Gur, R. E., Gur, R. C., Larsen, B., Mehta, K., Meisler, S. L., Murtha, K., Muschelli, J., Roalf, D. R., Sydnor, V. J., Valcarcel, A. M., Shinohara, R. T., Cieslak, M. & Satterthwaite, T. D. (2023). ModelArray: an R package for statistical analysis of fixel-wise data, _NeuroImage_, In press. https://doi.org/10.1016/j.neuroimage.2023.120037
+> Zhao, C., Tapera, T. M., Bagautdinova, J., Bourque, J., Covitz, S., Gur, R. E., Gur, R. C., Larsen, B., Mehta, K., Meisler, S. L., Murtha, K., Muschelli, J., Roalf, D. R., Sydnor, V. J., Valcarcel, A. M., Shinohara, R. T., Cieslak, M. & Satterthwaite, T. D. (2023). ModelArray: an R package for statistical analysis of fixel-wise data. _NeuroImage_, _271_, 120037. https://doi.org/10.1016/j.neuroimage.2023.120037
 
 
 ## Overview
@@ -42,7 +42,7 @@ Please cite our [NeuroImage paper](https://doi.org/10.1016/j.neuroimage.2023.120
 
 </center>
 
-ModelArray is packaged with the companion software [ConFixel](https://github.com/PennLINC/ConFixel) for converting fixel-wise data and voxel-wise data to the expected file format that ModelArray uses. Specifically, [ConFixel](https://github.com/PennLINC/ConFixel) is Python-based command-line interface software, and it converts between the original image format (`.mif` for fixel-wise data, NIfTI for voxel-wise data) and the HDF5 file format (`.h5`) used for ModelArray.
+ModelArray is packaged with the companion software [ConFixel](https://github.com/PennLINC/ConFixel) for converting fixel-wise data, voxel-wise data or greyordinate-wise data to the expected file format that ModelArray uses. Specifically, [ConFixel](https://github.com/PennLINC/ConFixel) is Python-based command-line interface software, and it converts between the original image format (`.mif` for fixel-wise data, NIfTI for voxel-wise data, CIFTI-2 for greyordinate-wise data) and the HDF5 file format (`.h5`) used for ModelArray.
 
 <!-- if there is any changes in this overview section, please also update ConFixel's frontpage! -->
 

diff --git a/README.md b/README.md
@@ -26,7 +26,8 @@ and beyond. Its features include:
     effects in lifespan data. `ModelArray` is also extensible to diverse
     models available in R;
 - Scalable for large-scale datasets;
-- Compatible with fixel-wise data and voxel-wise data.
+- Compatible with fixel-wise data, voxel-wise data, and
+  greyordinate-wise data.
 
 Please cite our [NeuroImage
 paper](https://doi.org/10.1016/j.neuroimage.2023.120037) if you use
@@ -36,8 +37,8 @@ paper](https://doi.org/10.1016/j.neuroimage.2023.120037) if you use
 > Gur, R. E., Gur, R. C., Larsen, B., Mehta, K., Meisler, S. L., Murtha,
 > K., Muschelli, J., Roalf, D. R., Sydnor, V. J., Valcarcel, A. M.,
 > Shinohara, R. T., Cieslak, M. & Satterthwaite, T. D. (2023).
-> ModelArray: an R package for statistical analysis of fixel-wise data,
-> *NeuroImage*, In press.
+> ModelArray: an R package for statistical analysis of fixel-wise data.
+> *NeuroImage*, *271*, 120037.
 > <https://doi.org/10.1016/j.neuroimage.2023.120037>
 
 ## Overview
@@ -50,12 +51,13 @@ paper](https://doi.org/10.1016/j.neuroimage.2023.120037) if you use
 
 ModelArray is packaged with the companion software
 [ConFixel](https://github.com/PennLINC/ConFixel) for converting
-fixel-wise data and voxel-wise data to the expected file format that
-ModelArray uses. Specifically,
+fixel-wise data, voxel-wise data or greyordinate-wise data to the
+expected file format that ModelArray uses. Specifically,
 [ConFixel](https://github.com/PennLINC/ConFixel) is Python-based
 command-line interface software, and it converts between the original
-image format (`.mif` for fixel-wise data, NIfTI for voxel-wise data) and
-the HDF5 file format (`.h5`) used for ModelArray.
+image format (`.mif` for fixel-wise data, NIfTI for voxel-wise data,
+CIFTI-2 for greyordinate-wise data) and the HDF5 file format (`.h5`)
+used for ModelArray.
 
 <!-- if there is any changes in this overview section, please also update ConFixel's frontpage! -->
 

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CLONE.html b/docs/CLONE.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/basic_r_intro.html b/docs/articles/basic_r_intro.html
diff --git a/docs/articles/container.html b/docs/articles/container.html
diff --git a/docs/articles/debugging.html b/docs/articles/debugging.html
diff --git a/docs/articles/doc_for_developer.html b/docs/articles/doc_for_developer.html
diff --git a/docs/articles/faq.html b/docs/articles/faq.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/installations.html b/docs/articles/installations.html
diff --git a/docs/articles/overview_structure.png b/docs/articles/overview_structure.png
diff --git a/docs/articles/voxel-wise_data.html b/docs/articles/voxel-wise_data.html
diff --git a/docs/articles/walkthrough.html b/docs/articles/walkthrough.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
   installations: installations.html
   voxel-wise_data: voxel-wise_data.html
   walkthrough: walkthrough.html
-last_built: 2023-03-17T01:19Z
+last_built: 2023-12-14T23:49Z
 urls:
   reference: https://pennlinc.github.io/ModelArray/reference
   article: https://pennlinc.github.io/ModelArray/articles

diff --git a/docs/reference/ModelArray.gam.html b/docs/reference/ModelArray.gam.html
diff --git a/docs/reference/ModelArray.html b/docs/reference/ModelArray.html
diff --git a/docs/reference/ModelArray.lm.html b/docs/reference/ModelArray.lm.html