From a31ffa8e7c7de33ac151df8cd2274aa98c0db4c2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?= Date: Tue, 1 Aug 2023 21:41:23 -0400 Subject: [PATCH 1/4] DOC: Increase consistency in SlicerDMRI citation message Increase consistency in SlicerDMRI citation message: - Prefer using https over http for web addresses when available. - Use the website to refer to SlicerDMRI instead of the source code repository. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index b86c981..1b15b7a 100644 --- a/README.md +++ b/README.md @@ -63,6 +63,6 @@ Install [WMA](https://github.com/SlicerDMRI/whitematteranalysis) and run - How to cite the [Slicer platform](http://wiki.slicer.org/slicerWiki/index.php/CitingSlicer) - An example of how to cite SlicerDMRI (modify the first part of the sentence according to your use case): - "We performed diffusion MRI tractography and/or analysis and/or visualization in 3D Slicer (www.slicer.org) via the SlicerDMRI project (dmri.slicer.org) ([Norton et al. 2017](http://cancerres.aacrjournals.org/content/77/21/e101)). + "We performed diffusion MRI tractography and/or analysis and/or visualization in 3D Slicer (https://www.slicer.org/) via the SlicerDMRI project (https://dmri.slicer.org/) ([Norton et al. 2017](http://cancerres.aacrjournals.org/content/77/21/e101)). Norton, I., Essayed, WI., Zhang, F., Pujol, S., Yarmarkovich, A., Golby, AJ., Kindlmann, G., Wassermann, D., Estepar, RSJ., Rathi, Y., Pieper, S., Kikinis, R., Johnson, HJ., Westin, C-F., and O'Donnell, LJ. SlicerDMRI: Open Source Diffusion MRI Software for Brain Cancer Research. Cancer Research 77(21), e101-e103, 2017." From 2fc56db2102cc5918efea301ecc152a7a7ce8978 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?= Date: Thu, 3 Aug 2023 16:40:13 -0400 Subject: [PATCH 2/4] DOC: Prefer using https over http for SlicerDMRI web address Prefer using https over http for web SlicerDMRI web address. --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 1b15b7a..483927b 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # O'Donnell Research Group (ORG) Fiber Clustering White Matter Atlas -This Github repository provides an anatomically curated white matter atlas to enable consistent white matter tract parcellation across different populations ([Zhang et al. 2018](https://doi.org/10.1016/j.neuroimage.2018.06.027)). In brief, the atlas contains **an anatomical fiber tract parcellation** into 58 deep white matter tracts including major long range association and projection tracts, commissural tracts, and tracts related to the brainstem and cerebellar connections, plus 198 short and medium range superficial fiber clusters organized into 16 categories according to the brain lobes they connect. In addition, the atlas contains a **whole brain white matter parcellation** of the entire white matter into 800 fiber clusters. For more information, please see the videos, links, and related introductions on the [Atlases](http://dmri.slicer.org/atlases) page in [SlicerDMRI](http://dmri.slicer.org). +This Github repository provides an anatomically curated white matter atlas to enable consistent white matter tract parcellation across different populations ([Zhang et al. 2018](https://doi.org/10.1016/j.neuroimage.2018.06.027)). In brief, the atlas contains **an anatomical fiber tract parcellation** into 58 deep white matter tracts including major long range association and projection tracts, commissural tracts, and tracts related to the brainstem and cerebellar connections, plus 198 short and medium range superficial fiber clusters organized into 16 categories according to the brain lobes they connect. In addition, the atlas contains a **whole brain white matter parcellation** of the entire white matter into 800 fiber clusters. For more information, please see the videos, links, and related introductions on the [Atlases](https://dmri.slicer.org/atlases) page in [SlicerDMRI](https://dmri.slicer.org). ## 1. ORG Atlas Visualization @@ -12,7 +12,7 @@ This Github repository provides an anatomically curated white matter atlas to en - Locate an MRB file in the decompressed folder (e.g., *T_AF.mrb* for the arcuate fasciculus tract). - Note: The list of all anatomical tracts can be found [here](Tracts-in-ORG-800FC-100HCP.md). - Drag and drop the selected MRB file onto 3D Slicer for visualization. - - Note: SlicerDMRI needs to be installed in 3D Slicer for this visualization (see [here](http://dmri.slicer.org/download/) for installation instructions). + - Note: SlicerDMRI needs to be installed in 3D Slicer for this visualization (see [here](https://dmri.slicer.org/download/) for installation instructions). - Note: Use the Models module in 3D Slicer to visualize each individual fiber cluster. Click the *Include Fibers* checkbox on the top left of the Models module to show the clusters in the *Scene* panel, and then click the *eye* icon to turn on or off the visibility of a cluster. ### 1.2. Visualization of the whole brain 800-cluster parcellation From 6199559c79512a72e21e366089ea520a6118f444 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?= Date: Tue, 1 Aug 2023 21:43:35 -0400 Subject: [PATCH 3/4] DOC: Use Slicer's new documentation web addresses Use Slicer's new documentation web addresses: most notably, refer to the documentation in Slicer's readthedocs site. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 483927b..dad8ed8 100644 --- a/README.md +++ b/README.md @@ -60,7 +60,7 @@ Install [WMA](https://github.com/SlicerDMRI/whitematteranalysis) and run #### Please include the following text (or similar) and citations for using Slicer and SlicerDMRI -- How to cite the [Slicer platform](http://wiki.slicer.org/slicerWiki/index.php/CitingSlicer) +- How to cite the [Slicer platform](https://slicer.readthedocs.io/en/latest/user_guide/about.html#how-to-cite) - An example of how to cite SlicerDMRI (modify the first part of the sentence according to your use case): "We performed diffusion MRI tractography and/or analysis and/or visualization in 3D Slicer (https://www.slicer.org/) via the SlicerDMRI project (https://dmri.slicer.org/) ([Norton et al. 2017](http://cancerres.aacrjournals.org/content/77/21/e101)). From 055994fc4e651fa32397242d63f653ad811d02dc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?= Date: Tue, 1 Aug 2023 21:45:55 -0400 Subject: [PATCH 4/4] DOC: Use current Cancer Research journal web address Use current Cancer Research journal web address. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index dad8ed8..4ad43a6 100644 --- a/README.md +++ b/README.md @@ -63,6 +63,6 @@ Install [WMA](https://github.com/SlicerDMRI/whitematteranalysis) and run - How to cite the [Slicer platform](https://slicer.readthedocs.io/en/latest/user_guide/about.html#how-to-cite) - An example of how to cite SlicerDMRI (modify the first part of the sentence according to your use case): - "We performed diffusion MRI tractography and/or analysis and/or visualization in 3D Slicer (https://www.slicer.org/) via the SlicerDMRI project (https://dmri.slicer.org/) ([Norton et al. 2017](http://cancerres.aacrjournals.org/content/77/21/e101)). + "We performed diffusion MRI tractography and/or analysis and/or visualization in 3D Slicer (https://www.slicer.org/) via the SlicerDMRI project (https://dmri.slicer.org/) ([Norton et al. 2017](https://aacrjournals.org/cancerres/article/77/21/e101/662618)). Norton, I., Essayed, WI., Zhang, F., Pujol, S., Yarmarkovich, A., Golby, AJ., Kindlmann, G., Wassermann, D., Estepar, RSJ., Rathi, Y., Pieper, S., Kikinis, R., Johnson, HJ., Westin, C-F., and O'Donnell, LJ. SlicerDMRI: Open Source Diffusion MRI Software for Brain Cancer Research. Cancer Research 77(21), e101-e103, 2017."