fdt merge requestshttps://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests2024-03-27T09:53:54+00:00https://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/25BF: Update GUI to call `$FSLDIR/bin/eddy`, remove "Use GPU version" checkbox2024-03-27T09:53:54+00:00Paul McCarthyBF: Update GUI to call `$FSLDIR/bin/eddy`, remove "Use GPU version" checkboxThe `eddy` executable files were renamed to `eddy_cpu` and `eddy_cuda10.2` about two years ago, and a helper script simply called `eddy` was added, which will call one or the other, depending on whether or not a GPU is present.The `eddy` executable files were renamed to `eddy_cpu` and `eddy_cuda10.2` about two years ago, and a helper script simply called `eddy` was added, which will call one or the other, depending on whether or not a GPU is present.https://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/23ENH: Add `--premat` and `--postmat` options to `vecreg`2024-01-18T11:47:01+00:00Paul McCarthyENH: Add `--premat` and `--postmat` options to `vecreg`Add `--premat` and `--postmat` options to `vecreg` so that, when warping a vector or tensor field, an initial affine transform can also be provided. This is useful when working with MMORF, as MMORF saves its displacement fields _without_...Add `--premat` and `--postmat` options to `vecreg` so that, when warping a vector or tensor field, an initial affine transform can also be provided. This is useful when working with MMORF, as MMORF saves its displacement fields _without_ encoding any source-to-reference affine transfornm.https://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/21MNT: Fix dc calls2023-02-08T13:16:35+00:00Paul McCarthyMNT: Fix dc callsReplace `dc` calls with syntax that will work on all platforms (`dc -` is unsupported on new macOS)Replace `dc` calls with syntax that will work on all platforms (`dc -` is unsupported on new macOS)https://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/20BF: fix argument parsing2022-10-06T12:37:54+01:00Paul McCarthyBF: fix argument parsingReported here: https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;c858e06b.2112
and here: https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;495523a1.2210
I forgot to apply the fix after the first report.
Occasionally `bedpostx_p...Reported here: https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;c858e06b.2112
and here: https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;495523a1.2210
I forgot to apply the fix after the first report.
Occasionally `bedpostx_postproc_gpu.sh` will be passed an empty string as an argument, which causes the `-z "$2"` test to return false. The test needs to check whether the `$2` variable is set, as opposed to testing whether it is non-empty.https://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/19BF: Remove LD_LIBRARY_PATH as breaking script on cluster2022-09-30T09:35:54+01:00Matthew WebsterBF: Remove LD_LIBRARY_PATH as breaking script on clusterThe modification of LD_LIBRARY_PATH https://git.fmrib.ox.ac.uk/fsl/fdt/-/blob/2202.3/CUDA/bedpostx_gpu#L7 is breaking the `cp` ( e.g. https://git.fmrib.ox.ac.uk/fsl/fdt/-/blob/2202.3/CUDA/bedpostx_gpu#L235 ) command on the cluster with e...The modification of LD_LIBRARY_PATH https://git.fmrib.ox.ac.uk/fsl/fdt/-/blob/2202.3/CUDA/bedpostx_gpu#L7 is breaking the `cp` ( e.g. https://git.fmrib.ox.ac.uk/fsl/fdt/-/blob/2202.3/CUDA/bedpostx_gpu#L235 ) command on the cluster with error message:
`cp: relocation error: /lib64/libacl.so.1: symbol getxattr, version ATTR_1.0 not defined in file libattr.so.1 with link time reference`
Removing this line allows `bedpostx_gpu` to run to completionhttps://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/18RF: Change Makefile so that gpu build *only* compiles/installs CUDA binaries....2022-05-24T14:11:53+01:00Paul McCarthyRF: Change Makefile so that gpu build *only* compiles/installs CUDA binaries. Everything else is done via cpu buildhttps://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/17BF: shared lib name has changed2022-05-24T12:08:22+01:00Paul McCarthyBF: shared lib name has changedhttps://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/16MNT: Need to include thrust/[host|device]_vector2022-02-16T12:25:24+00:00Paul McCarthyMNT: Need to include thrust/[host|device]_vectorOtherwise compilation fails on CUDA >= 11.4Otherwise compilation fails on CUDA >= 11.4https://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/15mnt/conda2021-11-29T17:14:14+00:00Paul McCarthymnt/condahttps://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/14BF: move wildcard out of quotes2021-03-02T14:59:02+00:00Taylor Hanayiktaylor.hanayik@ndcn.ox.ac.ukBF: move wildcard out of quotesTaylor Hanayiktaylor.hanayik@ndcn.ox.ac.ukTaylor Hanayiktaylor.hanayik@ndcn.ox.ac.ukhttps://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/10Master2021-01-27T18:59:09+00:00Duncan MortimerMasterMain change is to switch to new fsl_sub CUDA selection method. Have left it as an option for the user to override this. Nothing added to select correct CUDA SDK, but don't see how that could be hardcoded.
Also quoted rm command input wh...Main change is to switch to new fsl_sub CUDA selection method. Have left it as an option for the user to override this. Nothing added to select correct CUDA SDK, but don't see how that could be hardcoded.
Also quoted rm command input where it is a variable for safety.
Have not quoted the rm ${$}\* and rm ${$}bin\* as I don't understand the syntax.
No longer mail the user on completion.
fsl_sub is now used to delete jobs, check on existence of cluster queues (no longer hard coded to expect SGE) and the presence of CUDA (environment variable no longer required that specifies the queue, and can find CUDA on a machine that isn't using a cluster submission suite).https://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/13BF: Fix improperly quoted command2021-01-07T13:47:36+00:00Paul McCarthyBF: Fix improperly quoted commandhttps://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/12BF: Correctly concatenate array options2020-12-29T15:52:01+00:00Matthew WebsterBF: Correctly concatenate array optionsThe current "other" options code will _not_ correctly concatenate options and instead will effectively _drop_ them, leading to a failure in the test: fsl_course/fdt/bedpostx_cpu. The updated code should correctly concatenate the array va...The current "other" options code will _not_ correctly concatenate options and instead will effectively _drop_ them, leading to a failure in the test: fsl_course/fdt/bedpostx_cpu. The updated code should correctly concatenate the array variables, as with the gopts variable later on in the code.Matthew WebsterMatthew Websterhttps://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/11Fix compilation issue with limits.h2020-11-14T09:35:15+00:00Moises FernandezFix compilation issue with limits.hFixing issue described on https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;2b74023.2006Fixing issue described on https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;2b74023.2006Moises FernandezMoises Fernandezhttps://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/8BF: change linking orde2020-07-22T12:51:22+01:00Taylor Hanayiktaylor.hanayik@ndcn.ox.ac.ukBF: change linking ordeFSL 6.0.4Taylor Hanayiktaylor.hanayik@ndcn.ox.ac.ukTaylor Hanayiktaylor.hanayik@ndcn.ox.ac.ukhttps://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/7Add -db flag to set maximum offset in b-value2020-07-17T13:40:20+01:00Michiel Cottaarmichiel.cottaar@ndcn.ox.ac.ukAdd -db flag to set maximum offset in b-valueMakes select_dwi_vols a bit more flexible.
Seems to work on HCP data.Makes select_dwi_vols a bit more flexible.
Seems to work on HCP data.https://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/5select_dwi_vols fix requested by MC2020-01-24T14:31:37+00:00Matthew Websterselect_dwi_vols fix requested by MChttps://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/4Activate the --kurtdir flag2019-12-16T12:31:49+00:00Michiel Cottaarmichiel.cottaar@ndcn.ox.ac.ukActivate the --kurtdir flagThis is code originally from @saad and edited by me. It extends the previous --kurt flag to compute the kurtosis along the 3 eigenvalues (i.e., allows the eigenvalues to change linearly as a function of b-value). This is a simplified ver...This is code originally from @saad and edited by me. It extends the previous --kurt flag to compute the kurtosis along the 3 eigenvalues (i.e., allows the eigenvalues to change linearly as a function of b-value). This is a simplified version of the kurtosis model, which also allows deviations from a diffusion tensor model within a single shell (i.e., for a single b-value).
To prevent the kurtosis from going to +/-infinite, when the diffusion is very small, a prior is added to the kurtosis with a mean of 0 and variance of 1.
I'll open a seperate pull request to pyfeeds-tests to add some tests.
TODO: enable --wls flag to work with --kurtdir (currently it crashes) <- not doing this yet, added an error if both --wls and --kurtdir flags are sethttps://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/3Use standard master rule eval2019-12-06T15:37:14+00:00Matthew WebsterUse standard master rule evalhttps://git.fmrib.ox.ac.uk/fsl/fdt/-/merge_requests/2Remove fslconfig dependency2019-11-29T14:51:32+00:00Matthew WebsterRemove fslconfig dependency