Merge pull request #167 from DCAN-Labs/more_edits

Added more GitHub tips and made formatting edits

docs/bibsnet-testing.md

@@ -159,7 +159,7 @@ Look at the averaged T1w and T2w to ensure it looks “normal” (`derivatives/p
 
   * There shouldn’t be “bad” average anatomical images here if all of the above conditions are satisfied.
 
-  * If there are, post a Github issue [here](https://github.com/DCAN-Labs/BIBSnet/issues).
+  * If there are, post a GitHub issue [here](https://github.com/DCAN-Labs/BIBSnet/issues).
 
 
 Look at the cropped T1w and T2w to ensure it is not overcropped or undercropped. (`derivatives/prebibsnet/sub-*/ses-*/cropped/T(1|2)w/sub-*_ses-*_000(0|1).nii.gz`)
@@ -169,7 +169,7 @@ Look at the cropped T1w and T2w to ensure it is not overcropped or undercropped.
 
 Look at both resizing outputs to see if either alignment (xfms[non-ACPC] or ACPC_align) option leads to a properly aligned T1w and T2w (`derivatives/prebibsnet/sub-*/ses-*/resized/(ACPC_align|xfms)/`)
 
-  * If neither image pair looks aligned to each other, post a Github issue [here](https://github.com/DCAN-Labs/BIBSnet/issues). We only need one of the pairs to be aligned to each other. It’s okay if one of them looks bad, we’re making a choice in the next step.
+  * If neither image pair looks aligned to each other, post a GitHub issue [here](https://github.com/DCAN-Labs/BIBSnet/issues). We only need one of the pairs to be aligned to each other. It’s okay if one of them looks bad, we’re making a choice in the next step.
 
   * Note: be sure to check different areas throughout the brain.
 
@@ -178,7 +178,7 @@ Look at the BIBSnet input and ensure it chose the properly aligned pair of T1w a
 
   * To do this, I open the corresponding files in the `derivatives/prebibsnet/sub-*/ses-*/resized/(ACPC_align|xfms)/` and `derivatives/bibsnet/sub-*/ses-*/input/` to ensure the T1ws match the T1ws and the T2ws match the T2ws.
 
-  * If it chose the wrong pair, post a Github issue [here](https://github.com/DCAN-Labs/BIBSnet/issues).
+  * If it chose the wrong pair, post a GitHub issue [here](https://github.com/DCAN-Labs/BIBSnet/issues).
 
   * For the sake of time, you can copy and rename the properly aligned image pair into that directory, mirroring the naming schema present in that directory.
 
@@ -187,18 +187,18 @@ Look at the BIBSnet output and ensure there are not any holes in the segmentatio
 
   * Load into your image viewer of choice the BIBSnet input file and the BIBSnet output file with the segmentation on top. 
 
-  * If there are holes in the segmentation and you used the correct resources for you job, post a Github issue [here](https://github.com/DCAN-Labs/BIBSnet/issues).
+  * If there are holes in the segmentation and you used the correct resources for you job, post a GitHub issue [here](https://github.com/DCAN-Labs/BIBSnet/issues).
 
   * It is okay if the chirality does not match, this will *hopefully* be fixed in postBIBSnet.
 
 
 Look at the chirality corrected outputs to ensure the chirality matches the proper hemisphere and there are no holes. (`/derivatives/precomputed/sub-*/ses-*/chirality_correction/`)
 
-  * If the segmentation doesn’t have the proper chirality, post a Github issue [here](https://github.com/DCAN-Labs/BIBSnet/issues).
+  * If the segmentation doesn’t have the proper chirality, post a GitHub issue [here](https://github.com/DCAN-Labs/BIBSnet/issues).
 
-  * If the segmentation has holes, post a Github issue [here](https://github.com/DCAN-Labs/BIBSnet/issues).
+  * If the segmentation has holes, post a GitHub issue [here](https://github.com/DCAN-Labs/BIBSnet/issues).
 
 
 Look at the precomputed file to make sure it’s aligned to the T1 (T1 and T2 model, T1-only model) or the T2 (T2-only model).
 
-  * If misaligned, post a Github issue [here](https://github.com/DCAN-Labs/BIBSnet/issues).
+  * If misaligned, post a GitHub issue [here](https://github.com/DCAN-Labs/BIBSnet/issues).

docs/bwas.md

@@ -4,4 +4,4 @@ BWAS are used to link brain structure and function to behavior. It uses massive
 
 Documentation can be found [here.](https://polyneuro-risk-score.readthedocs.io/en/latest/PolyNeuro_Risk_Scores/)
 
-Version-controlled code can be found on [Github](https://github.com/DCAN-Labs/BWAS)
+Version-controlled code can be found on [GitHub](https://github.com/DCAN-Labs/BWAS)

docs/cifti-matrix.md

@@ -6,4 +6,4 @@ This code takes the BOLD time series data for a single voxel and correlates it w
 
 This code can be found on MSI at `/home/faird/shared/code/internal/utilities/cifti_connectivity`
 
-Version-controlled code and documentation can be found on [Github.](https://github.com/DCAN-Labs/cifti-connectivity)
+Version-controlled code and documentation can be found on [GitHub.](https://github.com/DCAN-Labs/cifti-connectivity)

docs/coding-practices.md

@@ -30,7 +30,7 @@ A Bronze certification broadly entails the following:
 
 * License and readme
 
-* Issue tracking (typically through Github)
+* Issue tracking (typically through GitHub)
 
 * Some sort of testing 
 

docs/containers.md

@@ -57,7 +57,7 @@ Assuming you have a github repository that has the dockerfile to build your imag
 
 - Run `git clone html-to-repo --branch name-of-branch-to-clone`
 
-- If you are asked for your credentials, enter your github username, then open Github and go to Settings -> Developer Settings (located at very bottom) -> Personal Access Tokens and click Generate New Token. Enter the new token ID as your password.
+- If you are asked for your credentials, enter your github username, then open GitHub and go to Settings -> Developer Settings (located at very bottom) -> Personal Access Tokens and click Generate New Token. Enter the new token ID as your password.
 
 Navigate into the cloned repository 
 

docs/dcm2bids.md

@@ -83,6 +83,6 @@ Watch: [Dcm2bids DCAN tutorial recording](https://drive.google.com/drive/folders
         
         - For more information on arguments, see the ReadMe section on Optional Arguments [here](https://github.com/DCAN-Labs/abcd-dicom2bids).
         
-        - For running multiple subjects, it is advised to use a [wrapper ](wrappers.md)to submit one subject/session at a time. There is a wrapper for tier 1 here: `/home/faird/shared/code/internal/utilities/slurm_pipeline_wrappers/slurm_abcd-hcp-pipeline_scripts` and a wrapper for tier 2 here: `/home/faird/shared/code/internal/utilities/slurm_pipeline_wrappers/slurm_abcd-hcp-pipeline_scripts_with_s3_routines_with_ses`
+        - For running multiple subjects, it is advised to use a [wrapper ](wrappers.md)to submit one subject/session at a time. There is a wrapper for tier 1 here: `/home/faird/shared/code/internal/utilities/SLURM_wrappers/slurm_abcd-hcp-pipeline_scripts` and a wrapper for tier 2 here: `/home/faird/shared/code/internal/utilities/SLURM_wrappers/slurm_abcd-hcp-pipeline_scripts_with_s3_routines_with_ses`
             
             * Note: if you do not have access to the faird share, please fill out [this contact form](https://innovation.umn.edu/developmental-cognition-and-neuroimaging-lab/contact-us/) to request access.

docs/git-commands.md

@@ -1,12 +1,12 @@
 # Common Git Commands
 
-This page contains common commands used to work with Github repositories via git. This is by no means an exhaustive list of commands. 
+This page contains common commands used to work with GitHub repositories via git. This is by no means an exhaustive list of commands. 
 
 ## Basics 
 
 `git clone https://url-to-repo OR [email protected]:repo/location.git`
 
-- Clone a github repo. Two methods: HTTPS or SSH. SSH is recommended as it will not require a token every time you interact with the repo (push/pull/etc) on MSI. Learn how to set up SSH with Github [on this page](github-quick-guide.md). If you do use HTTPS on MSI you will need to [create a personal access token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens#creating-a-personal-access-token-classic) and enter it every time you interact with the repo. 
+- Clone a GitHub repo. Two methods: HTTPS or SSH. SSH is recommended as it will not require a token every time you interact with the repo (push/pull/etc) on MSI. Learn how to set up SSH with GitHub [on this page](github-quick-guide.md). If you do use HTTPS on MSI you will need to [create a personal access token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens#creating-a-personal-access-token-classic) and enter it every time you interact with the repo. 
 - If you would like to only clone a specific branch, add `-b branch_name --single-branch` after `clone`.
 
 `git status`
@@ -15,7 +15,7 @@ This page contains common commands used to work with Github repositories via git
 
 `git checkout -b branch_name`
 
-- Move to a new/different github branch. If the branch already exists, do not include the `-b`. 
+- Move to a new/different GitHub branch. If the branch already exists, do not include the `-b`. 
 
 - `git branch new_branch_name` also creates a new branch but doesn't also move you to the new branch
 
@@ -33,13 +33,13 @@ This page contains common commands used to work with Github repositories via git
 
 `git push`
 
-- Push your commit to the github repo
+- Push your commit to the GitHub repo
 
 - If you made a new branch locally, to add it to the origin, run `git push --set-upstream origin branch-name`
 
 `git pull`
 
-- Pull the contents of the github repo to your local computer 
+- Pull the contents of the GitHub repo to your local computer 
 
 ## Advanced
 
@@ -52,7 +52,7 @@ git checkout branch_to_update
 git rebase main
 ```
 
-If a branch name changed on Github but it still has the old name locally and you can no longer push to/pull from the old branch name:
+If a branch name changed on GitHub but it still has the old name locally and you can no longer push to/pull from the old branch name:
 
 ```
 git branch -m old_name new_name

docs/github-quick-guide.md

@@ -80,7 +80,7 @@ Click "+" in the top right, select "New repository," fill in details, and click
 
 **Clone the Repository:**
 
-On the Github page of your repository, select the green Code button and select HTTPS or SSH then click the double square icon to copy the URL to your clipboard.
+On the GitHub page of your repository, select the green Code button and select HTTPS or SSH then click the double square icon to copy the URL to your clipboard.
 Open the terminal on your local computer where you want to clone the repository and run the following command to clone the repository:
 
 ```

docs/github-tips.md

@@ -17,8 +17,14 @@
 5. Put a README.md within all your codebases, even if you are the only person using it.
     - You will forget how to run you own code, trust me.
 6. Get a DOI for your codebase if it is being used by others.
-    - This is usually done via zenodo.
+    - This is usually done via [zenodo](zenodo.md).
     - People will be able to credit you and reference specific commits with this.
+7. [Add a README.md to your profile](https://docs.github.com/en/account-and-profile/setting-up-and-managing-your-github-profile/customizing-your-profile/managing-your-profile-readme).
+    - Include your linked in, projects your working on, your focus, other websites, recent publications, etc
+    - More information on how to personalize your GitHub profile can be found [here](https://docs.github.com/en/account-and-profile/setting-up-and-managing-your-github-profile/customizing-your-profile/personalizing-your-profile).
+8. Keep your branches updated
+    - Frequently [pull to and sync from your local branch](https://docs.github.com/en/desktop/working-with-your-remote-repository-on-github-or-github-enterprise/syncing-your-branch-in-github-desktop)
+    - When intending to submit a [pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests), merge with the branch you're intending to submit the PR to locally before initiating the request. This ensures you won't have any merge conflicts.
 
 ## Watch a Repo 
 

docs/motion-regressor.md

@@ -1,6 +1,6 @@
 # Analyzing Motion Regressor 
 
-Motion regression is performed on neuroimaging data to reduce motion-related artifacts in the signal. This method focuses on using MATLAB scripts to process the regressor files and identify motion artifacts related to respiration. More information about the scripts can be found on the [Github repo.](https://github.com/DCAN-Labs/movement_regressors_power_plots)
+Motion regression is performed on neuroimaging data to reduce motion-related artifacts in the signal. This method focuses on using MATLAB scripts to process the regressor files and identify motion artifacts related to respiration. More information about the scripts can be found on the [GitHub repo.](https://github.com/DCAN-Labs/movement_regressors_power_plots)
 
 **NOTE:** If you are trying to use this analysis on fmriprep/nibabies outputs, you will need to save your working directory to find the movement regressor files. 
 

docs/pipelines.md

@@ -126,7 +126,7 @@ ${singularity} run --cleanenv \
 
 ## 3. ABCD-HCP-BIDS
 
-Read: [abcd-hcp-pipeline @ Github](https://github.com/DCAN-Labs/abcd-hcp-pipeline)
+Read: [abcd-hcp-pipeline @ GitHub](https://github.com/DCAN-Labs/abcd-hcp-pipeline)
 
 
 Read: [abcd-hcp-pipeline @ ABCC ReadTheDocs](https://collection3165.readthedocs.io/en/stable/pipeline/)
@@ -283,7 +283,7 @@ ${singularity} run –cleanenv \
 ## 6. DCAN Infant
 
 
-Read: [infant-abcd-bids-pipeline @ Github](https://github.com/DCAN-Labs/infant-abcd-bids-pipeline)
+Read: [infant-abcd-bids-pipeline @ GitHub](https://github.com/DCAN-Labs/infant-abcd-bids-pipeline)
 
 
 This fMRI minimal preprocessing pipeline is based on Washington University's HCP Pipeline. Many changes were made to accomodate the differences in the developing brain of infants. Notably:
@@ -341,7 +341,7 @@ ${infant_abcd_bids_pipeline} \
 
 ## 7. BIBSnet
 
-BIBSnet is a segmentation pipeline including stages prebibsnet, bibsnet, and postbibsnet.
+BIBSnet is a segmentation pipeline including stages `prebibsnet`, `bibsnet`, and `postbibsnet`.
 
 Example command: 
 
@@ -357,7 +357,7 @@ Example command:
 ```
 
 
- _NOTE: IT IS NOT RECOMMENDED TO RUN BIBSNET OUTSIDE OF THE CONTAINER._
+ _NOTE: IT IS NOT RECOMMENDED TO RUN BIBSnet OUTSIDE OF THE CONTAINER._
 
 
 For troubleshooting information, see [the Testing BIBSnet page.](bibsnet-testing.md)

docs/requests.md

@@ -14,7 +14,7 @@ Do you need help transferring data to/from/between MSI servers/storage systems?
 
 Are there any issues with this guide or things that are unclear?
 
-* Post an issue [on Github](https://github.com/DCAN-Labs/dcan-labs-informational-guide/issues) to suggest improvements and ask questions
+* Post an issue [on GitHub](https://github.com/DCAN-Labs/dcan-labs-informational-guide/issues) to suggest improvements and ask questions
 
 Are you having any issues with any of our pipelines? 
 

docs/template-matching.md

@@ -10,4 +10,4 @@ Template matching is a method of network mapping that leverages commonly observe
 
 The code can be found on MSI at `/home/faird/shared/code/internal/analytics/compare_matrices_to_assign_networks`
 
-Version-controlled code and documentation can be found on [Github.](https://github.com/DCAN-Labs/compare_matrices_to_assign_networks)
+Version-controlled code and documentation can be found on [GitHub.](https://github.com/DCAN-Labs/compare_matrices_to_assign_networks)