From 95a46d5f4b78be095f232c2509359d3e360da262 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri, 2 Aug 2019 15:00:08 -0400
Subject: [PATCH 01/12] ENH: Neurodocker script to create docker container with
 patched linkchecker

---
 tools/linkchecker-docker/neurodocker-build.sh | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100755 tools/linkchecker-docker/neurodocker-build.sh

diff --git a/tools/linkchecker-docker/neurodocker-build.sh b/tools/linkchecker-docker/neurodocker-build.sh
new file mode 100755
index 0000000000..8b9aa66ccc
--- /dev/null
+++ b/tools/linkchecker-docker/neurodocker-build.sh
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+# A script to build docker image with desired patched linkchecker
+# using neurodocker
+
+# TODOs:
+#   - minimize image (currently >500MB) using reprozip
+#     see https://github.com/kaczmarj/neurodocker/#minimize-existing-docker-image
+#     for instructions
+
+# tag for patched linkchecker -- will also serve our image version
+version="9.4.0.anchorfix1"
+# docker image build
+build=1
+
+neurodocker generate docker \
+    --base neurodebian:nd100 \
+    --pkg-manager apt \
+    --install python-pip python-requests python-dnspython python-setuptools python-wheel \
+    --run "sed -e 's,^deb ,deb-src ,g' /etc/apt/sources.list > /etc/apt/sources.list.d/deb-sources.list \
+    && apt-get update \
+    && apt-get build-dep -y linkchecker \
+    && pip install pyxdg https://github.com/yarikoptic/linkchecker/archive/$version.zip \
+    && mkdir ~/.linkchecker && echo '[AnchorCheck]' > ~/.linkchecker/linkcheckerrc \
+    " \
+    --entrypoint /usr/local/bin/linkchecker \
+| docker build -t yarikoptic/linkchecker:$version-$build -

From 649e5ec250f5c1f48d401773db108c36995c5a4a Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri, 2 Aug 2019 15:01:50 -0400
Subject: [PATCH 02/12] ENH: place built site/ into workspace and run
 linkchecker from a dedicated docker image as a separate job

---
 .circleci/config.yml | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index b8aa208d9b..3c3b8c8a99 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -25,6 +25,18 @@ jobs:
           command: pipenv run mkdocs build --clean --strict --verbose
       - store_artifacts:
           path: site
+      - persist_to_workspace:
+          root: .
+          paths: site
+
+  linkchecker:
+    docker:
+      - image: yarikoptic/linkchecker:9.4.0.anchorfix1-1
+    steps:
+      - attach_workspace:
+          at: ~/build
+      # Image already has linkchecker as the entry point
+      - run: ~/build/site
 
 # Auto changelog collector
   github-changelog-generator:
@@ -127,6 +139,7 @@ workflows:
   search_build:
     jobs:
       - build
+      - linkchecker
       - github-changelog-generator:
           filters:
                branches:

From 5107ae091f70670e0973dd3a061ca88ec59fd22e Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 5 Aug 2019 09:46:34 -0400
Subject: [PATCH 03/12] BF: state that linkchecker requires build (otherwise
 workspace is empty!)

---
 .circleci/config.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 3c3b8c8a99..d7fd464fb0 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -139,7 +139,9 @@ workflows:
   search_build:
     jobs:
       - build
-      - linkchecker
+      - linkchecker:
+          requires:
+            - build
       - github-changelog-generator:
           filters:
                branches:

From 64faa855f7e509a5e36711f9b0d17081666f90fa Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri, 2 Aug 2019 15:15:36 -0400
Subject: [PATCH 04/12] BF: add linkchecker command (entered image), and chmod
 entire ~ to be readable -- demanded by linkchecker

- note: it is important to have trailing / after site/ for linkchecker
---
 .circleci/config.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index d7fd464fb0..2d9a1f4cf6 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -35,8 +35,10 @@ jobs:
     steps:
       - attach_workspace:
           at: ~/build
-      # Image already has linkchecker as the entry point
-      - run: ~/build/site
+      - run:
+          command: |
+            chmod a+rX -R ~
+            linkchecker ~/build/site/
 
 # Auto changelog collector
   github-changelog-generator:

From f795519bd1a4fe3caec75e0369288617ff3639b3 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 5 Aug 2019 10:19:47 -0400
Subject: [PATCH 05/12] BF: fixed up #anchored references in two files

---
 src/04-modality-specific-files/03-electroencephalography.md   | 4 ++--
 .../04-intracranial-electroencephalography.md                 | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/04-modality-specific-files/03-electroencephalography.md
index 93fd73675d..36314b4290 100644
--- a/src/04-modality-specific-files/03-electroencephalography.md
+++ b/src/04-modality-specific-files/03-electroencephalography.md
@@ -197,7 +197,7 @@ required columns are channel `name`, `type` and `units` in this specific order.
 Channel names should furthermore appear in the table in the same order they do
 in the EEG data file. Any number of additional columns may be provided to
 provide additional information about the channels. Note that electrode
-positions should not be added to this file, but to [`*_electrodes.tsv`](./03-electroencephalography.md#electrodes-description-electrodes-tsv).
+positions should not be added to this file, but to [`*_electrodes.tsv`](./03-electroencephalography.md#electrodes-description-_electrodestsv).
 
 The columns of the Channels description table stored in `*_channels.tsv` are:
 
@@ -272,7 +272,7 @@ sub-<label>/
 File that gives the location of EEG electrodes. Note that coordinates are
 expected in cartesian coordinates according to the `EEGCoordinateSystem` and
 `EEGCoordinateSystemUnits` fields in `*_coordsystem.json`. **If an
-`*_electrodes.tsv` file is specified, a [`*_coordsystem.json`](#coordinate-system-json-coordsystem-json)
+`*_electrodes.tsv` file is specified, a [`*_coordsystem.json`](#coordinate-system-json-_coordsystemjson)
 file MUST be specified as well**. The order of the required columns in the
 `*_electrodes.tsv` file MUST be as listed below.
 
diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
index 0cc1b79608..739b74046a 100644
--- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md
+++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
@@ -392,7 +392,7 @@ Fields relating to the iEEG electrode positions:
 
 | Field name                          | Definition                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
 | :---------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
-| iEEGCoordinateSystem                | REQUIRED. Defines the coordinate system for the iEEG electrodes. See [Appendix VIII](../99-appendices/08-coordinate-systems.md) for a list of restricted keywords. If positions correspond to pixel indices in a 2D image (of either a volume-rendering, surface-rendering, operative photo, or operative drawing), this must be "Pixels". For more information, see the section on [2D coordinate systems](../04-modality-specific-files/04-intracranial-electroencephalography.md#Allowed-2D-coordinate-systems). |
+| iEEGCoordinateSystem                | REQUIRED. Defines the coordinate system for the iEEG electrodes. See [Appendix VIII](../99-appendices/08-coordinate-systems.md) for a list of restricted keywords. If positions correspond to pixel indices in a 2D image (of either a volume-rendering, surface-rendering, operative photo, or operative drawing), this must be "Pixels". For more information, see the section on [2D coordinate systems](#allowed-2d-coordinate-systems). |
 | iEEGCoordinateUnits                 | REQUIRED. Units of the \_electrodes.tsv, MUST be "m", "mm", "cm" or "pixels".                                                                                                                                                                                                                                                                                                                                                                                                                                       |
 | iEEGCoordinateSystemDescription     | RECOMMENDED. Freeform text description or link to document describing the iEEG coordinate system system in detail (e.g., "Coordinate system with the origin at anterior commissure (AC), negative y-axis going through the posterior commissure (PC), z-axis going to a mid-hemisperic point which lies superior to the AC-PC line, x-axis going to the right").                                                                                                                                                    |
 | iEEGCoordinateProcessingDescription | RECOMMENDED. Has any post-processing (such as projection) been done on the electrode positions (e.g., "surface_projection", "none").                                                                                                                                                                                                                                                                                                                                                                                |
@@ -417,7 +417,7 @@ upper left pixel and (N,0) corresponding to the lower left pixel.
 
 If electrode positions are known in multiple coordinate systems (e.g., MRI, CT
 and MNI), these spaces can be distinguished by the optional `[_space-<label>]`
-field, see the [`*_electrodes.tsv`-section](../04-modality-specific-files/04-intracranial-electroencephalography.md#electrode-description-space-label-electrodes-tsv)
+field, see the [`*_electrodes.tsv`-section](#electrode-description-_electrodestsv)
 for more information. Note that the `[_space-<label>]` fields must correspond
 between `*_electrodes.tsv` and `*_coordsystem.json` if they refer to the same
 data.

From 002c365e2bada399919e08896ac8cf3b8eb17037 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 5 Aug 2019 10:33:37 -0400
Subject: [PATCH 06/12] BF(workaround): run linkchecker in a single thread

apparently my anchor fix to linkchecker is not complete.  In multithreaded mode
(the beauty of linkchecker) it brings up false positives reporting some anchors
which are valid.  See e.g.

https://circleci.com/gh/bids-standard/bids-specification/911?utm_campaign=vcs-integration-link&utm_medium=referral&utm_source=github-build-link
---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 2d9a1f4cf6..29ab538f3e 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -38,7 +38,7 @@ jobs:
       - run:
           command: |
             chmod a+rX -R ~
-            linkchecker ~/build/site/
+            linkchecker -t 1 ~/build/site/
 
 # Auto changelog collector
   github-changelog-generator:

From 7d329ff77e92d96a99a5723c9e4966fd8b102972 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 5 Aug 2019 10:33:55 -0400
Subject: [PATCH 07/12] BF: URL to mindboggle should have no www.

---
 src/99-appendices/08-coordinate-systems.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/08-coordinate-systems.md b/src/99-appendices/08-coordinate-systems.md
index 674b20c0a0..504a72bcc8 100644
--- a/src/99-appendices/08-coordinate-systems.md
+++ b/src/99-appendices/08-coordinate-systems.md
@@ -122,7 +122,7 @@ the units are assumed to be mm.
 | NIHPD                                               | Pediatric templates generated from the NIHPD sample. Available for different age groups (4.5–18.5 y.o., 4.5–8.5 y.o., 7–11 y.o., 7.5–13.5 y.o., 10–14 y.o., 13–18.5 y.o. This template also comes in either -symmetric or -asymmetric flavor. [http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1](http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1) |
 | Talairach                                           | Piecewise linear scaling of the brain is implemented as described in TT88. [http://www.talairach.org/](http://www.talairach.org/)                                                                                                                                                                                                                                |
 | OASIS30AntsOASISAnts                                | [https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436](https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436)                                                                                                                                                                                                                               |
-| OASIS30Atropos                                      | [http://www.mindboggle.info/data.html](http://www.mindboggle.info/data.html)                                                                                                                                                                                                                                                                                     |
+| OASIS30Atropos                                      | [http://mindboggle.info/data.html](http://mindboggle.info/data.html)                                                                                                                                                                                                                                                                                     |
 | ICBM452AirSpace                                     | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" with "linear transforms of the subjects into the atlas space using a 12-parameter affine transformation" [http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml](http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml)                              |
 | ICBM452Warp5Space                                   | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" "based on a 5th order polynomial transformation into the atlas space" [http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml](http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml)                                                                 |
 | IXI549Space                                         | Reference space defined by the average of the "549 (...) subjects from the IXI dataset" linearly transformed to ICBM MNI 452.Used by SPM12. [http://www.brain-development.org/](http://www.brain-development.org/)                                                                                                                                               |

From 1d73e7b630990a4368ed60ff6e971a7a393d3dfe Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 5 Aug 2019 10:41:07 -0400
Subject: [PATCH 08/12] BF: Cognitive atlas urls went from /term/ to /task/ for
 the rest state task example

---
 src/04-modality-specific-files/02-magnetoencephalography.md | 2 +-
 src/04-modality-specific-files/03-electroencephalography.md | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md
index d1b34fbb29..e4b594cec6 100644
--- a/src/04-modality-specific-files/02-magnetoencephalography.md
+++ b/src/04-modality-specific-files/02-magnetoencephalography.md
@@ -75,7 +75,7 @@ Whenever possible, please avoid using ad-hoc wording.
 | SoftwareVersions       | RECOMMENDED. Manufacturer’s designation of the acquisition software.                                                                                                                                                                                                            |
 | TaskDescription        | RECOMMENDED. Description of the task.                                                                                                                                                                                                                                           |
 | Instructions           | RECOMMENDED. Text of the instructions given to participants before the scan. This is not only important for behavioral or cognitive tasks but also in resting state paradigms (e.g. to distinguish between eyes open and eyes closed).                                          |
-| CogAtlasID             | RECOMMENDED. URL of the corresponding [Cognitive Atlas](http://www.cognitiveatlas.org/) term that describes the task (e.g. Resting State with eyes closed "[http://www.cognitiveatlas.org/term/id/trm_54e69c642d89b](http://www.cognitiveatlas.org/term/id/trm_54e69c642d89b)") |
+| CogAtlasID             | RECOMMENDED. URL of the corresponding [Cognitive Atlas](http://www.cognitiveatlas.org/) term that describes the task (e.g. Resting State with eyes closed "[http://www.cognitiveatlas.org/task/id/trm_54e69c642d89b](http://www.cognitiveatlas.org/task/id/trm_54e69c642d89b)") |
 | CogPOID                | RECOMMENDED. URL of the corresponding [CogPO](http://www.cogpo.org/) term that describes the task (e.g. Rest "[http://wiki.cogpo.org/index.php?title=Rest](http://wiki.cogpo.org/index.php?title=Rest)")                                                                        |
 | DeviceSerialNumber     | RECOMMENDED. The serial number of the equipment that produced the composite instances. A pseudonym can also be used to prevent the equipment from being identifiable, as long as each pseudonym is unique within the dataset.                                                   |
 
diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/04-modality-specific-files/03-electroencephalography.md
index 36314b4290..1e6cda5655 100644
--- a/src/04-modality-specific-files/03-electroencephalography.md
+++ b/src/04-modality-specific-files/03-electroencephalography.md
@@ -104,7 +104,7 @@ Whenever possible, please avoid using ad hoc wording.
 | SoftwareVersions       | RECOMMENDED. Manufacturer's designation of the acquisition software.                                                                                                                                                                                                              |
 | TaskDescription        | RECOMMENDED. Description of the task.                                                                                                                                                                                                                                             |
 | Instructions           | RECOMMENDED. Text of the instructions given to participants before the scan. This is not only important for behavioral or cognitive tasks but also in resting state paradigms (e.g., to distinguish between eyes open and eyes closed).                                           |
-| CogAtlasID             | RECOMMENDED. URL of the corresponding [Cognitive Atlas](http://www.cognitiveatlas.org/) term that describes the task (e.g., Resting State with eyes closed "[http://www.cognitiveatlas.org/term/id/trm_54e69c642d89b](http://www.cognitiveatlas.org/term/id/trm_54e69c642d89b)"). |
+| CogAtlasID             | RECOMMENDED. URL of the corresponding [Cognitive Atlas](http://www.cognitiveatlas.org/) term that describes the task (e.g., Resting State with eyes closed "[http://www.cognitiveatlas.org/task/id/trm_54e69c642d89b](http://www.cognitiveatlas.org/task/id/trm_54e69c642d89b)"). |
 | CogPOID                | RECOMMENDED. URL of the corresponding [CogPO](http://www.cogpo.org/) term that describes the task (e.g., Rest "[http://wiki.cogpo.org/index.php?title=Rest](http://wiki.cogpo.org/index.php?title=Rest)") .                                                                       |
 | DeviceSerialNumber     | RECOMMENDED. The serial number of the equipment that produced the composite instances. A pseudonym can also be used to prevent the equipment from being identifiable, as long as each pseudonym is unique within the dataset.                                                     |
 

From f461c2602510e41db9d19a4801ac38a4d59e3189 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 5 Aug 2019 10:44:15 -0400
Subject: [PATCH 09/12] BF: Replaced dead link to fdt_dtifit with URL to
 FDT/UserGuide

---
 .../01-magnetic-resonance-imaging-data.md                       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 77bbeb1d82..0723cbc5f5 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -385,7 +385,7 @@ dwi.nii file) and not the magnet’s coordinate system, which means that any
 rotations applied to dwi.nii also need to be applied to the corresponding bvec
 file.
 
-<sup>4</sup>[http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_dtifit.html](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_dtifit.html)
+<sup>4</sup>[https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#DTIFIT](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#DTIFIT)
 
 bvec example:
 

From e25ae72d5324d11d30a17e278867805d9944cb2f Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 5 Aug 2019 10:47:33 -0400
Subject: [PATCH 10/12] BF: Replace dead link to download of ICBM 452T1 to some
 lame 1 page .pdf describing differences

I found no better URL upon a quick search
---
 src/99-appendices/08-coordinate-systems.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/99-appendices/08-coordinate-systems.md b/src/99-appendices/08-coordinate-systems.md
index 504a72bcc8..ddca276279 100644
--- a/src/99-appendices/08-coordinate-systems.md
+++ b/src/99-appendices/08-coordinate-systems.md
@@ -123,8 +123,8 @@ the units are assumed to be mm.
 | Talairach                                           | Piecewise linear scaling of the brain is implemented as described in TT88. [http://www.talairach.org/](http://www.talairach.org/)                                                                                                                                                                                                                                |
 | OASIS30AntsOASISAnts                                | [https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436](https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436)                                                                                                                                                                                                                               |
 | OASIS30Atropos                                      | [http://mindboggle.info/data.html](http://mindboggle.info/data.html)                                                                                                                                                                                                                                                                                     |
-| ICBM452AirSpace                                     | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" with "linear transforms of the subjects into the atlas space using a 12-parameter affine transformation" [http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml](http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml)                              |
-| ICBM452Warp5Space                                   | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" "based on a 5th order polynomial transformation into the atlas space" [http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml](http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml)                                                                 |
+| ICBM452AirSpace                                     | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" with "linear transforms of the subjects into the atlas space using a 12-parameter affine transformation" [https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf](https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf)                              |
+| ICBM452Warp5Space                                   | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" "based on a 5th order polynomial transformation into the atlas space" [https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf](https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf)                                                                 |
 | IXI549Space                                         | Reference space defined by the average of the "549 (...) subjects from the IXI dataset" linearly transformed to ICBM MNI 452.Used by SPM12. [http://www.brain-development.org/](http://www.brain-development.org/)                                                                                                                                               |
 | fsaverage\[3&#124;4&#124;5&#124;6&#124;sym\]        | Images were sampled to the FreeSurfer surface reconstructed from the subject’s T1w image, and registered to an fsaverage template                                                                                                                                                                                                                                |
 | UNCInfant\[0&#124;1&#124;2\]V\[21&#124;22&#124;23\] | Infant Brain Atlases from Neonates to 1-   and 2-year-olds. [https://www.nitrc.org/projects/pediatricatlas](https://www.nitrc.org/projects/pediatricatlas)                                                                                                                                                                                                       |

From ef6801c58580981ff3294e69cb10ad1b15241cbb Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 5 Aug 2019 10:50:41 -0400
Subject: [PATCH 11/12] ENH: add a separate call to check external URLs

---
 .circleci/config.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 29ab538f3e..cae80bf17e 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -39,6 +39,9 @@ jobs:
           command: |
             chmod a+rX -R ~
             linkchecker -t 1 ~/build/site/
+            # check external separately by pointing to all *html so no
+            # failures for local file:/// -- yoh found no better way,
+            linkchecker -t 1 --check-extern --ignore-url 'file:///.*' --ignore-url https://fonts.gstatic.com ~/build/site/*html ~/build/site/*/*.html
 
 # Auto changelog collector
   github-changelog-generator:

From 54a346915031a594d4111c6e9ee2d96d49713190 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 5 Aug 2019 11:29:05 -0400
Subject: [PATCH 12/12] BF: fixed up introduced problems to tables alignment

---
 .../04-intracranial-electroencephalography.md | 14 ++++----
 src/99-appendices/08-coordinate-systems.md    | 32 +++++++++----------
 2 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
index 739b74046a..b44ec52169 100644
--- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md
+++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
@@ -390,13 +390,13 @@ General fields:
 
 Fields relating to the iEEG electrode positions:
 
-| Field name                          | Definition                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
-| :---------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
-| iEEGCoordinateSystem                | REQUIRED. Defines the coordinate system for the iEEG electrodes. See [Appendix VIII](../99-appendices/08-coordinate-systems.md) for a list of restricted keywords. If positions correspond to pixel indices in a 2D image (of either a volume-rendering, surface-rendering, operative photo, or operative drawing), this must be "Pixels". For more information, see the section on [2D coordinate systems](#allowed-2d-coordinate-systems). |
-| iEEGCoordinateUnits                 | REQUIRED. Units of the \_electrodes.tsv, MUST be "m", "mm", "cm" or "pixels".                                                                                                                                                                                                                                                                                                                                                                                                                                       |
-| iEEGCoordinateSystemDescription     | RECOMMENDED. Freeform text description or link to document describing the iEEG coordinate system system in detail (e.g., "Coordinate system with the origin at anterior commissure (AC), negative y-axis going through the posterior commissure (PC), z-axis going to a mid-hemisperic point which lies superior to the AC-PC line, x-axis going to the right").                                                                                                                                                    |
-| iEEGCoordinateProcessingDescription | RECOMMENDED. Has any post-processing (such as projection) been done on the electrode positions (e.g., "surface_projection", "none").                                                                                                                                                                                                                                                                                                                                                                                |
-| iEEGCoordinateProcessingReference   | RECOMMENDED. A reference to a paper that defines in more detail the method used to localize the electrodes and to post-process the electrode positions. .                                                                                                                                                                                                                                                                                                                                                           |
+| Field name                          | Definition                                                                                                                                                                                                                                                                                                                                                                                                                                  |
+| :---------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| iEEGCoordinateSystem                | REQUIRED. Defines the coordinate system for the iEEG electrodes. See [Appendix VIII](../99-appendices/08-coordinate-systems.md) for a list of restricted keywords. If positions correspond to pixel indices in a 2D image (of either a volume-rendering, surface-rendering, operative photo, or operative drawing), this must be "Pixels". For more information, see the section on [2D coordinate systems](#allowed-2d-coordinate-systems) |
+| iEEGCoordinateUnits                 | REQUIRED. Units of the \_electrodes.tsv, MUST be "m", "mm", "cm" or "pixels".                                                                                                                                                                                                                                                                                                                                                               |
+| iEEGCoordinateSystemDescription     | RECOMMENDED. Freeform text description or link to document describing the iEEG coordinate system system in detail (e.g., "Coordinate system with the origin at anterior commissure (AC), negative y-axis going through the posterior commissure (PC), z-axis going to a mid-hemisperic point which lies superior to the AC-PC line, x-axis going to the right").                                                                            |
+| iEEGCoordinateProcessingDescription | RECOMMENDED. Has any post-processing (such as projection) been done on the electrode positions (e.g., "surface_projection", "none").                                                                                                                                                                                                                                                                                                        |
+| iEEGCoordinateProcessingReference   | RECOMMENDED. A reference to a paper that defines in more detail the method used to localize the electrodes and to post-process the electrode positions. .                                                                                                                                                                                                                                                                                   |
 
 ### Recommended 3D coordinate systems
 
diff --git a/src/99-appendices/08-coordinate-systems.md b/src/99-appendices/08-coordinate-systems.md
index ddca276279..756d2c9ec8 100644
--- a/src/99-appendices/08-coordinate-systems.md
+++ b/src/99-appendices/08-coordinate-systems.md
@@ -112,21 +112,21 @@ below, the origin is at the AC and the orientation of the axes is RAS. Unless
 specified explicitly in the sidecar file in the `XXCoordinateSystemUnits` field,
 the units are assumed to be mm.
 
-| Coordinate System                                   | Description                                                                                                                                                                                                                                                                                                                                                      |
-| ---------------------------------------------------   | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------   |
-| MNI152Lin                                           | Also known as ICBM (version with linear coregistration) [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin)                                                                                                                                                                                       |
-| MNI152NLin6\[Sym&#124;Asym\]                        | Also known as ICBM 6th generation (non-linear coregistration). Used by SPM99 -   SPM8 and FSL (MNI152NLin6Sym). [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6)                                                                                                                           |
-| MNI152NLin2009\[a-c\]\[Sym&#124;Asym\]              | Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). It comes in either three different flavours each in symmetric or asymmetric version. [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009)                                                           |
-| MNIColin27                                          | Average of 27 T1 scans of a single subject [http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres](http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres)                                                                                                                                                                                            |
-| MNI305                                              | Also known as avg305.                                                                                                                                                                                                                                                                                                                                            |
-| NIHPD                                               | Pediatric templates generated from the NIHPD sample. Available for different age groups (4.5–18.5 y.o., 4.5–8.5 y.o., 7–11 y.o., 7.5–13.5 y.o., 10–14 y.o., 13–18.5 y.o. This template also comes in either -symmetric or -asymmetric flavor. [http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1](http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1) |
-| Talairach                                           | Piecewise linear scaling of the brain is implemented as described in TT88. [http://www.talairach.org/](http://www.talairach.org/)                                                                                                                                                                                                                                |
-| OASIS30AntsOASISAnts                                | [https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436](https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436)                                                                                                                                                                                                                               |
-| OASIS30Atropos                                      | [http://mindboggle.info/data.html](http://mindboggle.info/data.html)                                                                                                                                                                                                                                                                                     |
-| ICBM452AirSpace                                     | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" with "linear transforms of the subjects into the atlas space using a 12-parameter affine transformation" [https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf](https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf)                              |
-| ICBM452Warp5Space                                   | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" "based on a 5th order polynomial transformation into the atlas space" [https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf](https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf)                                                                 |
-| IXI549Space                                         | Reference space defined by the average of the "549 (...) subjects from the IXI dataset" linearly transformed to ICBM MNI 452.Used by SPM12. [http://www.brain-development.org/](http://www.brain-development.org/)                                                                                                                                               |
-| fsaverage\[3&#124;4&#124;5&#124;6&#124;sym\]        | Images were sampled to the FreeSurfer surface reconstructed from the subject’s T1w image, and registered to an fsaverage template                                                                                                                                                                                                                                |
-| UNCInfant\[0&#124;1&#124;2\]V\[21&#124;22&#124;23\] | Infant Brain Atlases from Neonates to 1-   and 2-year-olds. [https://www.nitrc.org/projects/pediatricatlas](https://www.nitrc.org/projects/pediatricatlas)                                                                                                                                                                                                       |
+| Coordinate System                                   | Description                                                                                                                                                                                                                                                                                                                                                       |
+| ---------------------------------------------------   | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| MNI152Lin                                           | Also known as ICBM (version with linear coregistration) [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin)                                                                                                                                                                                        |
+| MNI152NLin6\[Sym&#124;Asym\]                        | Also known as ICBM 6th generation (non-linear coregistration). Used by SPM99 -   SPM8 and FSL (MNI152NLin6Sym). [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6)                                                                                                                            |
+| MNI152NLin2009\[a-c\]\[Sym&#124;Asym\]              | Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). It comes in either three different flavours each in symmetric or asymmetric version. [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009)                                                            |
+| MNIColin27                                          | Average of 27 T1 scans of a single subject [http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres](http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres)                                                                                                                                                                                             |
+| MNI305                                              | Also known as avg305.                                                                                                                                                                                                                                                                                                                                             |
+| NIHPD                                               | Pediatric templates generated from the NIHPD sample. Available for different age groups (4.5–18.5 y.o., 4.5–8.5 y.o., 7–11 y.o., 7.5–13.5 y.o., 10–14 y.o., 13–18.5 y.o. This template also comes in either -symmetric or -asymmetric flavor. [http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1](http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1)  |
+| Talairach                                           | Piecewise linear scaling of the brain is implemented as described in TT88. [http://www.talairach.org/](http://www.talairach.org/)                                                                                                                                                                                                                                 |
+| OASIS30AntsOASISAnts                                | [https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436](https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436)                                                                                                                                                                                                                                |
+| OASIS30Atropos                                      | [http://mindboggle.info/data.html](http://mindboggle.info/data.html)                                                                                                                                                                                                                                                                                              |
+| ICBM452AirSpace                                     | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" with "linear transforms of the subjects into the atlas space using a 12-parameter affine transformation" [https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf](https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf) |
+| ICBM452Warp5Space                                   | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" "based on a 5th order polynomial transformation into the atlas space" [https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf](https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf)                                    |
+| IXI549Space                                         | Reference space defined by the average of the "549 (...) subjects from the IXI dataset" linearly transformed to ICBM MNI 452.Used by SPM12. [http://www.brain-development.org/](http://www.brain-development.org/)                                                                                                                                                |
+| fsaverage\[3&#124;4&#124;5&#124;6&#124;sym\]        | Images were sampled to the FreeSurfer surface reconstructed from the subject’s T1w image, and registered to an fsaverage template                                                                                                                                                                                                                                 |
+| UNCInfant\[0&#124;1&#124;2\]V\[21&#124;22&#124;23\] | Infant Brain Atlases from Neonates to 1-   and 2-year-olds. [https://www.nitrc.org/projects/pediatricatlas](https://www.nitrc.org/projects/pediatricatlas)                                                                                                                                                                                                        |
 
 ---