xtract merge requestshttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests2021-05-28T09:04:58+01:00https://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/19Xtract blueprint2021-05-28T09:04:58+01:00Shaun WarringtonXtract blueprintAdded xtract_blueprint for the calculation of connectivity blueprints.Added xtract_blueprint for the calculation of connectivity blueprints.FSL 6.0.5Shaun WarringtonShaun Warringtonhttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/18Wayorder2021-05-10T16:25:15+01:00Shaun WarringtonWayorderAdded wayorder option to allow for specific target orderingAdded wayorder option to allow for specific target orderingFSL 6.0.5Shaun WarringtonShaun Warringtonhttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/31Accept `xfms/standard2diff_warp` and `xfms/diff2standard_warp` for non-linear...2023-12-04T13:17:22+00:00Paul McCarthyAccept `xfms/standard2diff_warp` and `xfms/diff2standard_warp` for non-linear warpsThis MR updates `xtract` so that the default value for the `-stdwarp` option will be set to `xfms/standard2diff_warp.nii.gz` and `xfms/diff2standard_warp.nii.gz` _or_ `xfms/standard2diff.nii.gz` and `xfms/diff2standard.nii.gz`. The FDT G...This MR updates `xtract` so that the default value for the `-stdwarp` option will be set to `xfms/standard2diff_warp.nii.gz` and `xfms/diff2standard_warp.nii.gz` _or_ `xfms/standard2diff.nii.gz` and `xfms/diff2standard.nii.gz`. The FDT GUI saves non-linear warp files as `xfms/diff2standard_warp.nii.gz` / `xfms/standard2diff_warp.nii.gz`, so it makes sense for XTRACT to accept these file names.https://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/30fix make_subplots error2023-10-16T11:26:06+01:00Shaun Warringtonfix make_subplots errorShaun WarringtonShaun Warringtonhttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/29minor fix2023-03-09T16:25:40+00:00Shaun Warringtonminor fixShaun WarringtonShaun Warringtonhttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/28Minor updates2023-03-09T12:25:29+00:00Shaun WarringtonMinor updatesAdded target requirement to blueprint.
Added warnings about linear warp fields with xtract.Added target requirement to blueprint.
Added warnings about linear warp fields with xtract.Shaun WarringtonShaun Warringtonhttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/26Added xtract_qc, add subcortical to blueprint2023-03-06T12:34:30+00:00Shaun WarringtonAdded xtract_qc, add subcortical to blueprintShaun WarringtonShaun Warringtonhttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/25MNT: Removed xtract_qc install as per SW request2023-02-27T13:35:15+00:00Matthew WebsterMNT: Removed xtract_qc install as per SW requesthttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/24Minor fix2023-02-22T11:20:32+00:00Shaun WarringtonMinor fixShaun WarringtonShaun Warringtonhttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/22Baby xtract, fsl_sub updates, xtract_qc, plus minor fixes2023-02-10T12:42:04+00:00Shaun WarringtonBaby xtract, fsl_sub updates, xtract_qc, plus minor fixesAdded HUMAN_BABY option for xtract with neonate xtract protocols.
Resolved issues with fsl_sub and optimised job submission (added parallel cluster processing option).
Added xtract_qc - group-level quality controlAdded HUMAN_BABY option for xtract with neonate xtract protocols.
Resolved issues with fsl_sub and optimised job submission (added parallel cluster processing option).
Added xtract_qc - group-level quality controlShaun WarringtonShaun Warringtonhttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/20BF: Fix for gpu-submission when using the fsl_sub shell plugin2021-07-28T14:08:14+01:00Matthew WebsterBF: Fix for gpu-submission when using the fsl_sub shell pluginCurrently the xtract script will fail when submitting a gpu-task via the new fsl_sub shell plugin ( this isn't an issue for cluster-based submission, hence not spotted when using on FMRIB servers ). This simplest fix is to "call" comman...Currently the xtract script will fail when submitting a gpu-task via the new fsl_sub shell plugin ( this isn't an issue for cluster-based submission, hence not spotted when using on FMRIB servers ). This simplest fix is to "call" commands.txt via sh, this change should be effectively transparent for cluster submission.https://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/17Bug allow noninteger2020-11-05T08:44:01+00:00Shaun WarringtonBug allow nonintegerFixed IF statement when checking 'res' - now allows for non-integer values to be used.Fixed IF statement when checking 'res' - now allows for non-integer values to be used.Shaun WarringtonShaun Warringtonhttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/16Master2020-10-08T15:41:00+01:00Duncan MortimerMasterThis comprises two changes the most important of which is in commit 227748f3f740c6625876013062729dff5b6f5c02
which adds support for the new fsl_sub. As the new fsl_sub shell backend (e.g. no cluster) can parallelise over available cores ...This comprises two changes the most important of which is in commit 227748f3f740c6625876013062729dff5b6f5c02
which adds support for the new fsl_sub. As the new fsl_sub shell backend (e.g. no cluster) can parallelise over available cores I have removed all SGE checks.
The (redundant) selection of -q long.q has been removed as this won't work at BMRC
Now using --coprocessor=cuda to select a GPU queue
Second merge request is suggestions to improve security of the script by quoting variables when arguments to external commands. This avoids issues with users providing 'something; rm -rf /').
= '', ! = '' and x"" = x is all very old syntax - use -z and -n for empty and non-empty strings instead.
You could also consider replacing `` with $() which is modern shell syntax but this hasn't been done here as I didn't want to mask the other changes.
I decided not to quote "$FSLDIR/acommand" but this would be a wise change.https://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/15Added -species CUSTOM option to allow tractography in any species2020-09-08T12:21:25+01:00Shaun WarringtonAdded -species CUSTOM option to allow tractography in any speciesAdded "CUSTOM" as option for the `-species` flag, which requires the specification of the protocols folder `-p`, a structure list file `-str`, and the standard space template brain `-stdref`.Added "CUSTOM" as option for the `-species` flag, which requires the specification of the protocols folder `-p`, a structure list file `-str`, and the standard space template brain `-stdref`.Shaun WarringtonShaun Warringtonhttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/14Update Makefile2020-07-17T12:54:15+01:00Shaun WarringtonUpdate MakefileShaun WarringtonShaun Warringtonhttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/13XTRACT stats2020-07-17T10:58:00+01:00Shaun WarringtonXTRACT statsAdded xtract_stats script for summary tract-wise stats.
Changed location of xtract_data to $FSLDIR/dataAdded xtract_stats script for summary tract-wise stats.
Changed location of xtract_data to $FSLDIR/dataShaun WarringtonShaun Warringtonhttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/12Refspace2020-04-30T10:31:47+01:00Shaun WarringtonRefspaceAdded the option for users to run tractography in any reference space, e.g. T1 space.Added the option for users to run tractography in any reference space, e.g. T1 space.Shaun WarringtonShaun Warringtonhttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/11Tract subsets2020-04-28T11:25:09+01:00Shaun WarringtonTract subsetsAdded '-list' flag to show tract names.
Added option to select a subset of the pre-defined tracts from either Human or Macaque - user provides structure file with tract names or tract names and nsamples.
Additional small bug fixesAdded '-list' flag to show tract names.
Added option to select a subset of the pre-defined tracts from either Human or Macaque - user provides structure file with tract names or tract names and nsamples.
Additional small bug fixesShaun WarringtonShaun Warringtonhttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/10Update README.md2020-02-26T09:05:56+00:00Shaun WarringtonUpdate README.mdShaun WarringtonShaun Warringtonhttps://git.fmrib.ox.ac.uk/fsl/xtract/-/merge_requests/9Update README.md2020-02-26T09:04:56+00:00Shaun WarringtonUpdate README.md