1.2.4

Release Notes

Bugfixes, an additional iteration over Sentry reporting and some relevant ME-EPI updates
(with thanks to @emdupre).

CHANGES

• [ENH] Update ME-EPI workflow to create optimal combination (#1263) @emdupre
• [MAINT] Merge master into multiecho (#1324) @effigies
• [ENH] Add echo-idx flag (#1355) @emdupre
• [FIX] Always run FreeSurfer interfaces that sink outside working directory (#1397) @effigies
• [ENH] Use Python 3.7 in Dockerfile (#1398) @effigies
• [DOC] Update contributing guide and add code of conduct (#1404) @emdupre
• [FIX] Calculate template transforms explicitly as RAS2RAS (#1399) @effigies
• [MAINT] Replace img.get_affine() -> img.affine (#1414) @oesteban
• [FIX] Truncating of sentry messages (#1417) @chrisfilo
• [ENH] Add fmriprep-docker execution environment (#1416) @chrisfilo
• [MAINT] Update indexed_gzip to handle small .nii.gz (#1421) @effigies
• [ENH] Group common issues with fingerprints (#1418) @chrisfilo
• [ENH] adding memory and cpu info to sentry logs (#1420) @chrisfilo
• [ENH] Use standard T2* map as coregistration target (#1383) @emdupre
• [ENH] Handle FreeSurfer subject directory preparation gracefully when run in parallel (#1413) @effigies
• [ENH] Make sure inputs are BIDS compliant before running fmriprep (#1419) @chrisfilo
• [ENH] Sentry event categorization propagation (#1422) @chrisfilo
• [MAINT] Require nipype >= 1.1.6 (#1426) @effigies
• [ENH] Omnibus multi-echo pull request (#1296) @effigies
• [ENH] Report memory overcommit policies (#1429) @effigies

1.2.3

Release Notes

Refactor of Sentry reporting, bug fixes, and added tests. With thanks to @sebnaze for contributions.

CHANGES

• [TEST] Utility functions for skipping/re-inserting non-steady-state volumes (#1382) @jdkent
• [FIX] Correctly populate right-hemisphere time series in CIFTI derivatives (#1378) @sebnaze
• [FIX] Restore original contour colors in reports (#1385) @oesteban
• [ENH] New sentry SDK (#1381) @chrisfilo
• [ENH] Sentry refinement (#1394) @chrisfilo

1.2.2

Release Notes

Several bug fixes. With thanks to Franz Liem, Nir Jacoby and Markus Handal Sneve for contributions.

CHANGES

• [FIX] Do not show --debug deprecation warning unless used (#1361) @effigies
• [FIX] Select consistent parcellation for producing aparcaseg derivatives (#1369) @nirjacoby
• [FIX] Count non-steady-state volumes even if sbref is passed (#1373) @effigies
• [ENH] Respect SliceEncodingDirection metadata (#1350) @fliem
• [ENH] Set maximum MELODIC components to 200 by default (#1366) @markushs
• [TEST] Verify LegacyMultiProc functionality (#1368) @effigies

1.2.1

Release Notes

Hotfix release (deployment system)

1.2.0

Release Notes

This release marks a substantial renaming of derivatives to conform to the BIDS Derivatives specification release candidate.

The most significant additional change is a substantial revision of BOLD skull-stripping, using a BOLD template constructed from many open datasets. Building off the work of Zhifang Ye (see #1050), the skull-stripping is now much more resilient to intensity inhomogeneity.

With many thanks to Ali Cohen, James Kent, Inge Amlien, Sebastian Urchs, and Zhifang Ye for contributions.

Changes

• [FIX] Missing BOLD reports (#1326) @oesteban
• [FIX] Ensure encoding when reading boilerplate (#1322) @alioco
• [FIX] Reportlets - bbregister vs flirtbbr (continues #1326) (#1328) @oesteban
• [FIX] Quick update to new template structure (#1330) @oesteban
• [FIX] Explicitly pass bold mask to AROMA (#1332) @jdkent
• [FIX] Missing report output - #1339 (#1346) @kasbohm
• [FIX] Remove non-steady-state volumes prior to ICA-AROMA (#1335) @jdkent
• [ENH] Store BOLD reference images (#1306) @oesteban
• [ENH] Deprecate --debug with --sloppy (#1347) @effigies
• [ENH] Conform confound regressor names to Derivatives RC2 (#1343) @effigies
• [ENH] Do not set KEEP_FILE_OPEN_DEFAULT (#1356) @effigies
• [ENH] Template-based masking of EPI boldrefs (#1321) @oesteban
• [DOC] Update BIDS-validator link (#1320) @surchs
• [DOC] add --bind method to singularity patch documentation (#1340) @jdkent
• [RF] Update anatomical derivatives for RC1 (#1325) @effigies
• [RF] Update functional derivatives for RC1 (#1333) @effigies
• [TST] Add heavily-nonuniform boldrefs for regression tests (#1329) @oesteban
• [TST] Fix expectations for CIFTI outputs & ds005 (#1344) @oesteban
• [MAINT] Ignore project settings files from popular python/code editors (#1336) @jdkent
• [CI] Deploy poldracklab/fmriprep:unstable tracking master (#1307) @effigies

1.1.8

Release Notes

Several bug fixes. This release is intended to be the last before we adopt BIDS-Derivatives RC1 conventions.

The next release version will be 1.2.0.

CHANGES

• [FIX] Enhance T2 contrast enhance_t2 in reference estimate (#1299) @effigies
• [FIX] Create template from one usable T1w image (#1305) @effigies
• [DOC] Switch to orig graph for init_bold_t2s_wf (#1298) @effigies
• [MAINT] Pin grabbit and pybids in setup.py (#1284) @oesteban

1.1.7

Release Notes

Several bug fixes. With thanks to Elizabeth Dupre and Romain Vala for contributions.

CHANGES

• [FIX] Revert FreeSurfer download URL (#1280) @chrisfilo
• [FIX] Default to 6 DoF for BOLD-T1w registration (#1286) @effigies
• [FIX] Only grab sbref images, not metadata (#1285) @effigies
• [FIX] QwarpPlusMinus renamed source_file to in_file (#1289) @effigies
• [FIX] Remove long paths from all LTA output files (#1274) @romainVala
• [ENH] Use single-band reference images when available (#1270) @effigies
• [DOC] Note GIFTI surface alignment (#1288) @effigies
• [REF] Split BOLD-T1w registration into calculation/application workflows (#1278) @emdupre
• [MAINT] Pin pybids and grabbit in Docker build (#1281) @chrisfilo

1.1.6

Release Notes

Hotfix release.

CHANGES

• [FIX] Typo in plugin config loading.

1.1.5

Release Notes

Improved documentation and minor bug fixes. With thanks to @jarodroland and @tsalo for contributions.

CHANGES

• [DOC] Replace --clearenv with correct --cleanenv flag (#1237) @jarodroland
• [DOC] De-indent to remove text from code block (#1238) @effigies
• [TST] Add enhance-and-skullstrip regression tests (#1074) @effigies
• [DOC] Clearly indicate that fMRIPrep requires Python 3.5+ (#1249) @oesteban
• [MAINT] Update PR template (#1239) @effigies
• [DOC] Set appropriate version in Zenodo citation (#1250) @oesteban
• [DOC] Updating long description (#1230) @oesteban
• [DOC] Add ME workflow description (#1253) @tsalo
• [FIX] Add memory annotation to ROIPlot interface (#1256) @jdkent
• [ENH] Write derivatives dataset_description.json (#1247) @effigies
• [DOC] Enable table text wrap and link docstrings to code on GitHub (#1258) @tsalo
• [DOC] Clarify language describing T1w image merging (#1269) @chrisfilo
• [FIX] Accommodate new template formats (#1273) @effigies
• [FIX] Permit overriding plugin config with CLI options (#1272) @effigies

1.1.4

Release Notes

A hotfix release for #1235. Additionally, notebooks have been synced with the latest version of that repository.

CHANGES

• [FIX] Verify first word of _cmd in dependency check (#1236)
• [DOC] Add two missing references (#1234)
• [ENH] Allow turning off random seeding for ANTs brain extraction (#919)