fsl_mrs merge requestshttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests2023-11-09T15:50:16+00:00https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/99CI: Versioneer update attempt 22023-11-09T15:50:16+00:00William ClarkeCI: Versioneer update attempt 2Fix for MR #97Fix for MR #97https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/109ENH: Allow multiple water reference metabolites.2024-02-07T13:22:55+00:00William ClarkeENH: Allow multiple water reference metabolites.- Multiple metabolites can now be specified as the water scaling metabolite
- Default water scaling metabolite is now PCr+Cr to add robustness to one of PCr or Cr not being fit.
- Improved error logging in `fsl_mrsi` when parallel proces...- Multiple metabolites can now be specified as the water scaling metabolite
- Default water scaling metabolite is now PCr+Cr to add robustness to one of PCr or Cr not being fit.
- Improved error logging in `fsl_mrsi` when parallel processing enabled.https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/108CI: Tags in validate2023-12-07T20:20:40+00:00William ClarkeCI: Tags in validateFix git tags appearing in validate CI jobs so that proper version numbers are used.Fix git tags appearing in validate CI jobs so that proper version numbers are used.https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/107BF: Summarise non-unique names2023-12-07T18:17:51+00:00William ClarkeBF: Summarise non-unique namesFixes issue in `fsl_mrs_summarise` where an infinite while loop was caused if no level of the paths were unique.Fixes issue in `fsl_mrs_summarise` where an infinite while loop was caused if no level of the paths were unique.https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/106BF: Windowed alignment2023-12-05T22:20:14+00:00William ClarkeBF: Windowed alignment- Bug fixes in windowed alignment.
- Minor tweaks to edit pipeline when using dynamic alignment.- Bug fixes in windowed alignment.
- Minor tweaks to edit pipeline when using dynamic alignment.https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/105CI: Add git to docker image2023-12-05T20:34:57+00:00William ClarkeCI: Add git to docker imageRequired for the validate job.Required for the validate job.https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/104Rel: 2.1.162023-11-25T21:57:21+00:00William ClarkeRel: 2.1.16https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/103Enh: Windowed phase frequency alignment2023-11-24T21:46:04+00:00William ClarkeEnh: Windowed phase frequency alignmentAdd windowed averaging option to the phase and frequency alignment tools.Add windowed averaging option to the phase and frequency alignment tools.https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/102Enh: Better dynamic visualisation2023-11-23T19:20:51+00:00William ClarkeEnh: Better dynamic visualisationImproved plots and reports for first stage dynamic fitting.Improved plots and reports for first stage dynamic fitting.https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/101CI: Remove curl from validate script2023-11-09T18:08:52+00:00William ClarkeCI: Remove curl from validate script-remove curl installation from docker validate-remove curl installation from docker validatehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/100CI: Upgrade versioneer to fix deploy issue2023-11-09T15:57:28+00:00William ClarkeCI: Upgrade versioneer to fix deploy issueUpgrade versioneer to 0.29Upgrade versioneer to 0.29https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/98Revert "Merge branch 'ci/versioneer' into 'master'"2023-11-09T15:45:24+00:00William ClarkeRevert "Merge branch 'ci/versioneer' into 'master'"This reverts merge request !97This reverts merge request !97https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/97CI: Version fix2023-11-09T15:40:34+00:00William ClarkeCI: Version fix- Update versioneer to 0.29- Update versioneer to 0.29https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/96CI: Build test Docker image2023-11-09T14:57:05+00:00William ClarkeCI: Build test Docker imageAdd Dockerfile and instructions for building test image. Add to CI actionAdd Dockerfile and instructions for building test image. Add to CI actionhttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/95BF: Fix CI Docker image2023-11-08T20:31:10+00:00William ClarkeBF: Fix CI Docker imageMove to micromamba docker and on the fly fsl tools install.Move to micromamba docker and on the fly fsl tools install.https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/94Enh: fMRS group level f-tests2023-09-06T12:02:14+01:00William ClarkeEnh: fMRS group level f-tests2.1.13 (Tuesday 5th August 2023)
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- Add group level f-tests to the `fmrs_stats` tool. First level f-contrasts are not yet implemented.
- Removed / retained indices after `fsl_mrs_proc unlike` (and related ...2.1.13 (Tuesday 5th August 2023)
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- Add group level f-tests to the `fmrs_stats` tool. First level f-contrasts are not yet implemented.
- Removed / retained indices after `fsl_mrs_proc unlike` (and related functions) are now listed in the NIfTI-MRS headers under the key "DIM_DYN Indices".https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/93BF: Fix example_usage notebooks.2023-08-10T14:41:07+01:00William ClarkeBF: Fix example_usage notebooks.Fixes minor issues in the example_usage notebooks.Fixes minor issues in the example_usage notebooks.https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/92BF: fsl_mrs_proc unlike and complete fsl_mrs_proc tests2023-08-10T11:00:23+01:00William ClarkeBF: fsl_mrs_proc unlike and complete fsl_mrs_proc testsFurther fixes to `fsl_mrs_proc unlike` and testing for all `fsl_mrs_proc` subcommands.Further fixes to `fsl_mrs_proc unlike` and testing for all `fsl_mrs_proc` subcommands.https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/91BF:fsl_mrs_proc unlike2023-08-08T15:53:20+01:00William ClarkeBF:fsl_mrs_proc unlikeFixed bug in `fsl_mrs_proc unlike` calling the wrong processing function.Fixed bug in `fsl_mrs_proc unlike` calling the wrong processing function.https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/merge_requests/90BF: Single coil covariance estimation for preproc pathways.2023-08-01T17:47:28+01:00William ClarkeBF: Single coil covariance estimation for preproc pathways.- Coil covariance estimation is now common across all inputs to `fsl_mrs_preproc` and `fsl_mrs_preproc_edit`.
- Fallback option to disable coil pre-whitening when it isn't possible to calculate.- Coil covariance estimation is now common across all inputs to `fsl_mrs_preproc` and `fsl_mrs_preproc_edit`.
- Fallback option to disable coil pre-whitening when it isn't possible to calculate.