| 72c6dfb | Oscar Esteban | 19 August 2022, 15:58:17 UTC | rel(22.0.3): Update CHANGES [skip ci] | 19 August 2022, 15:58:17 UTC |
| be663f0 | Oscar Esteban | 19 August 2022, 15:06:58 UTC | Merge pull request #1021 from nipreps/fix/999-reoriented-shape FIX: SynthStrip preprocessing miscalculating new shape after reorientation | 19 August 2022, 15:06:58 UTC |
| 4ddb34a | Oscar Esteban | 19 August 2022, 14:52:30 UTC | fix(synthstrip): shape calculation needs reordering The calculation of the new shape within the preprocessing for synthstrip was done in XYZ coordinates (i.e., extents for each physical axis were estimated and divided by the new 1mm pixel size). However, the new axis sizes did not account for the fact that data was stored with IJK -> XZY convention (corresponding to LIA). This PR accounts for this miscalculation. Resolves: #999. | 19 August 2022, 14:52:30 UTC |
| 96b9b97 | Oscar Esteban | 18 August 2022, 09:20:42 UTC | Merge pull request #1019 from psadil/issue-998_remove-slice-timing-correction remove slice-timing correction | 18 August 2022, 09:20:42 UTC |
| 854f21a | Oscar Esteban | 18 August 2022, 07:57:39 UTC | Merge pull request #1020 from nipreps/enh/datalad-get ENH: Add a new ``DataladIdentityInterface`` | 18 August 2022, 07:57:39 UTC |
| 1aa8002 | Oscar Esteban | 18 August 2022, 07:57:21 UTC | Merge pull request #1005 from eilidhmacnicol/fix/rodent-fd-defaults set rat-specific defaults for FD calculations | 18 August 2022, 07:57:21 UTC |
| d68baf6 | Patrick Sadil | 15 August 2022, 20:54:12 UTC | remove slice-timing correction | 18 August 2022, 07:55:29 UTC |
| 7ba8b79 | Oscar Esteban | 16 August 2022, 16:33:34 UTC | enh: add a new ``DataladIdentityInterface`` This interface runs some heuristics and tries to ``datalad get`` those files that look like broken symlinks in a datalad dataset. | 16 August 2022, 16:33:34 UTC |
| 54c6425 | Eilidh MacNicol | 03 August 2022, 16:14:52 UTC | fix: remove call to `opts.fd_radius` cli does not have an option for `fd_radius` | 16 August 2022, 08:19:41 UTC |
| 9b516ed | Eilidh MacNicol | 21 July 2022, 09:24:29 UTC | sty: flake8 | 16 August 2022, 08:19:41 UTC |
| 8040eae | Eilidh MacNicol | 18 July 2022, 16:23:40 UTC | fix: set default fd radius for rats | 16 August 2022, 08:19:41 UTC |
| a14998e | Oscar Esteban | 15 August 2022, 13:37:05 UTC | fix: deploy to Pypi in Circle | 16 August 2022, 06:33:00 UTC |
| 73f85c7 | Oscar Esteban | 15 August 2022, 13:02:01 UTC | fix: AFNI version check | 16 August 2022, 06:32:59 UTC |
| 0c07597 | Oscar Esteban | 15 August 2022, 12:35:27 UTC | rel(22.0.2): Update CHANGES [skip ci] | 16 August 2022, 06:32:59 UTC |
| 9fa8914 | Oscar Esteban | 15 August 2022, 20:07:51 UTC | maint: remove automation updating changelog | 15 August 2022, 20:07:51 UTC |
| d56d83e | Oscar Esteban | 15 August 2022, 20:05:44 UTC | doc: update license section so it shows folded ont the left-hand menu | 15 August 2022, 20:05:44 UTC |
| e17d9c6 | Oscar Esteban | 15 August 2022, 11:54:23 UTC | doc: remove codacy badge from README | 15 August 2022, 11:54:23 UTC |
| 5fdf70f | Oscar Esteban | 15 August 2022, 11:47:41 UTC | doc: fix RTD config yml | 15 August 2022, 11:47:41 UTC |
| 215cfd5 | NiPreps Bot | 15 August 2022, 09:48:37 UTC | auto: Update CHANGES [skip ci] | 15 August 2022, 09:48:37 UTC |
| d4eb090 | Oscar Esteban | 15 August 2022, 09:48:27 UTC | Merge pull request #1018 from nipreps/docs/fix-rtd DOC: Move readthedocs to use the config v2 file (YAML) | 15 August 2022, 09:48:27 UTC |
| 9410642 | Oscar Esteban | 15 August 2022, 09:25:20 UTC | fix: convert warnings into errors | 15 August 2022, 09:44:30 UTC |
| 727d5a3 | Oscar Esteban | 15 August 2022, 08:54:25 UTC | fix: make sure graphviz is installed | 15 August 2022, 08:54:25 UTC |
| 3139714 | Oscar Esteban | 15 August 2022, 08:54:07 UTC | fix: docs/requirements.txt has been removed | 15 August 2022, 08:54:07 UTC |
| 4e230e1 | Oscar Esteban | 15 August 2022, 08:43:12 UTC | docs: add readthedocs yaml config file | 15 August 2022, 08:43:12 UTC |
| 809d697 | Oscar Esteban | 15 August 2022, 08:42:53 UTC | maint: update infrastructure | 15 August 2022, 08:42:53 UTC |
| dc73553 | NiPreps Bot | 12 August 2022, 21:05:42 UTC | auto: Update CHANGES [skip ci] | 12 August 2022, 21:05:42 UTC |
| 4b7ea26 | Oscar Esteban | 12 August 2022, 21:05:32 UTC | Merge pull request #1017 from nipreps/fix/statsmodels-missing-dep MAINT: Fix statsmodels dependency, it is not optional | 12 August 2022, 21:05:32 UTC |
| 0cf3154 | Oscar Esteban | 12 August 2022, 16:58:35 UTC | fix: statsmodels is not optional | 12 August 2022, 16:58:35 UTC |
| 663ae9e | NiPreps Bot | 12 August 2022, 16:51:11 UTC | auto: Update CHANGES [skip ci] | 12 August 2022, 16:51:11 UTC |
| 71aa828 | Oscar Esteban | 12 August 2022, 16:50:59 UTC | Merge pull request #1016 from nipreps/fix/docker-build MAINT: Several critical updates to CircleCI and Docker images | 12 August 2022, 16:50:59 UTC |
| 1235088 | Oscar Esteban | 12 August 2022, 16:16:15 UTC | fix: pytests on circle | 12 August 2022, 16:47:52 UTC |
| 7abecc2 | Oscar Esteban | 12 August 2022, 15:46:08 UTC | fix: versioning in docker builds and packaging in Circle | 12 August 2022, 15:46:08 UTC |
| 0e35183 | Oscar Esteban | 12 August 2022, 15:26:33 UTC | maint: update machine images for CircleCI | 12 August 2022, 15:26:33 UTC |
| cb15908 | Oscar Esteban | 12 August 2022, 15:25:53 UTC | fix: remove __about__.py | 12 August 2022, 15:25:53 UTC |
| e1bd2cd | Oscar Esteban | 12 August 2022, 15:03:36 UTC | Merge pull request #1012 from nipreps/enh/new-rating-widget ENH: New version of the rating widget | 12 August 2022, 15:03:36 UTC |
| 60f0ee6 | Oscar Esteban | 12 August 2022, 12:54:11 UTC | enh: new version of the rating widget Changes with this PR: - Updates Bootstrapjs to version 5.0.2 - Updates jQuery to version 3.6.0 - Updates some components of bootstrap for the new version - Convert the rating widget into a range slider allowing interval ratings. - Reduce the space the widget takes with an accordion - Make the rating widget invisible at the start - Add a field for comments and a slider for rater confidence - Add a timer, which is also reported within the JSON object. Resolves: #1007. Resolves: #1008. | 12 August 2022, 14:27:52 UTC |
| 921635f | Oscar Esteban | 12 August 2022, 14:25:22 UTC | Merge pull request #1014 from nipreps/fix/update-t1w-metrics-test MAINT: Update the T1w IQMs to the new reference after #997 | 12 August 2022, 14:25:22 UTC |
| d7ba2e8 | Oscar Esteban | 12 August 2022, 14:24:05 UTC | fix: update the T1w IQMs to the new reference after #997 | 12 August 2022, 14:24:05 UTC |
| 895ff3d | Oscar Esteban | 12 August 2022, 14:00:35 UTC | Merge pull request #1013 from nipreps/fix/gha-packaging-tests MAINT: Fix failing tests as ``python setup.py`` is deprecated | 12 August 2022, 14:00:35 UTC |
| 1a49ef7 | Oscar Esteban | 12 August 2022, 13:55:47 UTC | docs: fix building on circleci | 12 August 2022, 13:55:47 UTC |
| 3d74a1c | Oscar Esteban | 12 August 2022, 13:34:20 UTC | maint: move to setuptools-scm | 12 August 2022, 13:49:37 UTC |
| 326c4da | Oscar Esteban | 12 August 2022, 13:15:54 UTC | fix: failing tests as python setup.py is deprecated | 12 August 2022, 13:15:54 UTC |
| e021008 | Oscar Esteban | 03 May 2022, 16:18:07 UTC | rel(22.0.1): Update CHANGES [skip ci] | 03 May 2022, 16:18:07 UTC |
| 0dd5545 | NiPreps Bot | 03 May 2022, 16:12:58 UTC | auto: Update CHANGES [skip ci] | 03 May 2022, 16:12:58 UTC |
| 89f4e03 | Oscar Esteban | 03 May 2022, 16:12:24 UTC | Merge pull request #997 from nipreps/fix/skull-stripped-t1w FIX: More lenient handling of skull-stripped datasets | 03 May 2022, 16:12:24 UTC |
| 1bf994e | Oscar Esteban | 03 May 2022, 15:59:10 UTC | fix: update FBER to return -1 if skull-stripped | 03 May 2022, 15:59:10 UTC |
| 58f07a3 | Oscar Esteban | 03 May 2022, 15:53:21 UTC | fix: corresponding change to qi1 index | 03 May 2022, 15:53:21 UTC |
| ac1980b | Oscar Esteban | 03 May 2022, 15:44:38 UTC | enh: more lenient handling of skull-stripped datasets after #994 | 03 May 2022, 15:44:38 UTC |
| e104b0c | Oscar Esteban | 03 May 2022, 09:01:41 UTC | rel(22.0.0): Update CHANGES [skip ci] | 03 May 2022, 09:01:41 UTC |
| e7c891a | Oscar Esteban | 03 May 2022, 08:47:54 UTC | rel(22.0.0): update .zenodo.json file | 03 May 2022, 08:47:54 UTC |
| 1a0fb8e | Oscar Esteban | 03 May 2022, 08:47:27 UTC | rel(22.0.0): add @jAchtzehn to contributors list [skip ci] | 03 May 2022, 08:47:27 UTC |
| 58ae2a4 | Oscar Esteban | 03 May 2022, 08:40:01 UTC | rel(22.0.0): Update CHANGES [skip ci] | 03 May 2022, 08:40:01 UTC |
| 19657b4 | NiPreps Bot | 03 May 2022, 08:19:52 UTC | auto: Update CHANGES [skip ci] | 03 May 2022, 08:19:52 UTC |
| eafac8c | Oscar Esteban | 03 May 2022, 08:19:38 UTC | Merge pull request #995 from nipreps/jAchtzehn/cnr FIX: Inconsistent API in anatomical CNR computation | 03 May 2022, 08:19:38 UTC |
| ae53945 | Oscar Esteban | 03 May 2022, 08:19:15 UTC | sty: remove unused import | 03 May 2022, 08:19:15 UTC |
| 8cd5d7e | Oscar Esteban | 03 May 2022, 07:36:20 UTC | sty: run black | 03 May 2022, 07:36:20 UTC |
| bf6c8d1 | jAchtzehn | 21 July 2021, 10:40:54 UTC | Changed standard deviation to variance in CNR formular | 03 May 2022, 07:34:36 UTC |
| 1ea4e3d | jAchtzehn | 21 July 2021, 10:25:58 UTC | Fixed inconsistent input spec in anatomical.py CNR computation | 03 May 2022, 07:34:36 UTC |
| d6baa9b | NiPreps Bot | 02 May 2022, 09:56:24 UTC | auto: Update CHANGES [skip ci] | 02 May 2022, 09:56:24 UTC |
| ef9ad97 | Oscar Esteban | 02 May 2022, 09:55:59 UTC | Merge pull request #994 from nipreps/fix/781 FIX: Check sanity of input data before extracting IQMs | 02 May 2022, 09:55:59 UTC |
| abf48fd | NiPreps Bot | 02 May 2022, 09:37:32 UTC | auto: Update CHANGES [skip ci] | 02 May 2022, 09:37:32 UTC |
| cb0c660 | Oscar Esteban | 02 May 2022, 09:37:22 UTC | Merge pull request #993 from nipreps/fix/965 ENH: Deprecate ``--start-idx`` / ``--stop-idx`` | 02 May 2022, 09:37:22 UTC |
| 42cb367 | Oscar Esteban | 02 May 2022, 09:35:20 UTC | fix: check sanity of input data before extracting IQMs Runs some minimal sanity checks on masks and input data before the metrics are extracted. Resolves: #781. | 02 May 2022, 09:35:20 UTC |
| 32889ab | Oscar Esteban | 02 May 2022, 09:13:00 UTC | enh: deprecate ``--start-idx`` / ``--stop-idx`` *MRIQC* is not a preprocessing tool. Therefore, there is no point in offering customizations that, instead, will open up the workflow to greater analytical variability. Instead of opening knobs for users to play, it is better to make a more complete reporting of outputs (e.g., #992). This PR disregards both flags from now on. Resolves: #965. | 02 May 2022, 09:13:00 UTC |
| e5cdc5a | NiPreps Bot | 02 May 2022, 06:57:42 UTC | auto: Update CHANGES [skip ci] | 02 May 2022, 06:57:42 UTC |
| 71e96d1 | Oscar Esteban | 02 May 2022, 06:57:05 UTC | Merge pull request #987 from nipreps/enh/synthstrip ENH: Add SynthStrip base module | 02 May 2022, 06:57:05 UTC |
| d1e8182 | Oscar Esteban | 29 April 2022, 04:34:05 UTC | fix: update metrics file | 29 April 2022, 04:34:05 UTC |
| 33a65bc | Oscar Esteban | 28 April 2022, 22:16:00 UTC | maint(circle): increase resources and activate DLC | 28 April 2022, 22:16:00 UTC |
| 05ed99d | Oscar Esteban | 28 April 2022, 17:21:31 UTC | Update anatomical.py | 28 April 2022, 17:21:31 UTC |
| 993cb54 | Oscar Esteban | 28 April 2022, 16:55:10 UTC | maint: get model from docker image | 28 April 2022, 16:55:10 UTC |
| cef9f67 | NiPreps Bot | 28 April 2022, 14:54:54 UTC | auto: Update CHANGES [skip ci] | 28 April 2022, 14:54:54 UTC |
| c462535 | Oscar Esteban | 28 April 2022, 14:54:39 UTC | Merge pull request #990 from nipreps/enh/miscelanous-improvements ENH: Improve building workflow message feedback | 28 April 2022, 14:54:39 UTC |
| 8f91b2b | NiPreps Bot | 28 April 2022, 14:53:59 UTC | auto: Update CHANGES [skip ci] | 28 April 2022, 14:53:59 UTC |
| b08a5a8 | Oscar Esteban | 28 April 2022, 14:53:48 UTC | Merge pull request #989 from nipreps/fix/drop-obliquity-verbose-reports FIX: Plot segmentations after dropping off-diagonal | 28 April 2022, 14:53:48 UTC |
| c9b4a1c | Oscar Esteban | 28 April 2022, 14:47:14 UTC | maint: add nitransforms as a dependency | 28 April 2022, 14:47:14 UTC |
| fa7fd8c | Oscar Esteban | 28 April 2022, 14:13:47 UTC | Update setup.cfg | 28 April 2022, 14:13:47 UTC |
| 9c77153 | Oscar Esteban | 28 April 2022, 14:10:35 UTC | fix: nitransforms pinned version to make it compatible with niworkflows | 28 April 2022, 14:10:35 UTC |
| a650937 | Oscar Esteban | 28 April 2022, 13:31:53 UTC | fix: plot segmentations after dropping off-diagonal | 28 April 2022, 13:35:07 UTC |
| 7458dd2 | Oscar Esteban | 28 April 2022, 09:48:35 UTC | fix: de-biasing by multiplication not working | 28 April 2022, 09:48:35 UTC |
| 0c58d5c | Oscar Esteban | 28 April 2022, 09:34:15 UTC | enh: improve building workflow message feedback | 28 April 2022, 09:34:15 UTC |
| 8c8840c | Oscar Esteban | 28 April 2022, 08:53:32 UTC | fix: licensing aspects | 28 April 2022, 08:53:32 UTC |
| af17a5a | Oscar Esteban | 28 April 2022, 07:59:28 UTC | enh: integrate within the full workflow Resolves: #933. Relates: #275, #554, #904. | 28 April 2022, 08:42:27 UTC |
| b724711 | Oscar Esteban | 27 April 2022, 21:18:03 UTC | enh: add SynthStrip base | 28 April 2022, 08:42:26 UTC |
| eb35d49 | NiPreps Bot | 28 April 2022, 08:41:49 UTC | auto: Update CHANGES [skip ci] | 28 April 2022, 08:41:49 UTC |
| 7c0ffc3 | Oscar Esteban | 28 April 2022, 08:41:24 UTC | Merge pull request #988 from nipreps/fix/deprecated-get_data FIX: Replace all deprecated ``nibabel.get_data()`` in anatomical module | 28 April 2022, 08:41:24 UTC |
| 65ef8bb | Oscar Esteban | 28 April 2022, 08:00:26 UTC | fix: replace all deprecated nibabel.get_data() in anatomical module | 28 April 2022, 08:00:26 UTC |
| 22f4044 | NiPreps Bot | 27 April 2022, 21:33:07 UTC | auto: Update CHANGES [skip ci] | 27 April 2022, 21:33:07 UTC |
| 581ede0 | Oscar Esteban | 27 April 2022, 21:32:29 UTC | Merge pull request #986 from nipreps/docs/nprocs-nthreads DOC: Improve documentation of ``--nprocs`` and ``--omp-nthreads`` | 27 April 2022, 21:32:29 UTC |
| 1eb4a74 | Oscar Esteban | 27 April 2022, 21:32:09 UTC | Update parser.py | 27 April 2022, 21:32:09 UTC |
| 92b6120 | Oscar Esteban | 27 April 2022, 13:43:19 UTC | enh: do not break lines | 27 April 2022, 13:43:19 UTC |
| 7c44781 | Oscar Esteban | 27 April 2022, 12:14:34 UTC | doc: improve documentation of ``--nprocs`` and ``--omp-nthreads`` Resolves: #849. | 27 April 2022, 12:14:34 UTC |
| f296065 | NiPreps Bot | 27 April 2022, 11:35:11 UTC | auto: Update CHANGES [skip ci] | 27 April 2022, 11:35:11 UTC |
| b60ebad | Oscar Esteban | 27 April 2022, 11:34:56 UTC | Merge pull request #984 from nipreps/enh/resource-monitor ENH: Add instrumentation to monitor resources | 27 April 2022, 11:34:56 UTC |
| 2696389 | Oscar Esteban | 27 April 2022, 10:49:25 UTC | maint(circleci): keep config and resources artifacts | 27 April 2022, 11:19:11 UTC |
| 9600ba7 | Oscar Esteban | 27 April 2022, 10:38:43 UTC | enh: produce png files at the end with --resource-monitor | 27 April 2022, 10:38:43 UTC |
| dc18692 | Oscar Esteban | 27 April 2022, 09:36:53 UTC | enh: less general setting of OMP_NUM_THREADS With this commit, I believe the VMem problems have been addressed. Resolves: #824. Related: #536. | 27 April 2022, 09:37:03 UTC |
| 48da82a | Oscar Esteban | 27 April 2022, 08:50:11 UTC | sty: run black | 27 April 2022, 08:50:11 UTC |
| e4bdd4e | Oscar Esteban | 27 April 2022, 08:48:59 UTC | fix: set OMP_NUM_THREADS=1 for master thread | 27 April 2022, 08:48:59 UTC |
| 3b3e5b0 | Oscar Esteban | 26 April 2022, 06:42:28 UTC | enh: incorporate new custom plugin | 27 April 2022, 08:39:48 UTC |
| 1f6bab4 | Oscar Esteban | 26 April 2022, 05:01:53 UTC | fix: initialize config in jailed workflow creation process | 26 April 2022, 06:44:17 UTC |
