Fixes to containers FSL dependency

[Lestropie]

Closes #2921.

See also https://github.com/MRtrix3/containers/pull/26, which includes changes necessary to produce the minified FSL dependency that this change then downloads from OSF.

While the container minification process intended to capture EddyQC's eddy_quad, the fact that it was not being properly executed was missed because dwifslpreproc does not return non-zero if it fails to execute.

Unfortunately I couldn't easily resolve just this one thing. I've ended up having to update the FSL version as well. Which is not fantastic for a patch MRtrix update, since there's some chance of a change in behaviour out of our control.

Regarding #2921, if this change is deemed acceptable I can push it to DockerHub as latest, which would make it easy for people to access immediately but without necessitating an MRtrix patch update.

[Lestropie]

@anaharrismatnez @jhuguetn: If you want to try mrtrix3/mrtrix3:eddyqcfix on DockerHub, that should allow dwifslpreproc to run eddy_quad.

[jhuguetn]

That's great, thanks @Lestropie! We will and will give you some feedback.
One single doubt after quickly reviewing the changes proposed in both ends (the image for building the minified FSL package and the main MRtrix3 image), in the former you used ANTs 2.5.2 while in the later the version of ANTs installed is the same as it was previously, release 2.3.4.
Could that have any undesired effect on the usage of the final MRtrix3 image that you might think of?

[Lestropie]

The minification container is now pulling a newer version of ANTs because the existing version was failing to compile (don't recall the specifics, but every time I tried to change one thing to get minification to work something else broke). However that change was only made for the sake of allowing me to re-run the minification process for FSL. That updated ANTs version has not been uploaded to OSF, and the MRtrix3 container continues to download the same minified version of ANTs as the 3.0.4 version of the container. That's intentional; I'd rather put off an update to a dependency until a minor version update.

[anaharrismatnez]

Thanks @Lestropie, we were able to run dwifslpreproc with eddy_quad perfectly using mrtrix3/mrtrix3:eddyqcfix. The only thing is that every time I run a command I get the following message any idea why it could be? /bin/bash: /opt/fsl/lib/libtinfo.so.6: no version information available (required by /bin/bash)

[daljit46]

Most likely, that warning is due to the issue mentioned in this post.

[Lestropie]

• [x] Resolve libtinfo.so warning before merging I saw this myself also, just forgot to list it here, and prioritised getting something functional for you.

[Lestropie]

@MRtrix3/mrtrix3-devs I would like to get this merged to clarify #3039.

Here is a terminal dump showing rectification of #2921; the output files in the last line would not be present if eddy_quad was not executed successfully:

[12:56 PM]-[robertes@9520l-003953-l]-[~/src/master]- |master U:1 ?:5 ✗|
$ git checkout container_eddyqc_fix
M   testing/binaries/data
Switched to branch 'container_eddyqc_fix'
Your branch is up to date with 'origin/container_eddyqc_fix'.

[12:56 PM]-[robertes@9520l-003953-l]-[~/src/master]- |container_eddyqc_fix U:1 ?:5 ✗|
$ docker build . -t mrtrix3:eddyqcfix
[+] Building 2453.4s (28/28) FINISHED                                                                  docker:default
...
 => => naming to docker.io/library/mrtrix3:eddyqcfix                                                             0.0s

[01:37 PM]-[robertes@9520l-003953-l]-[~/src/master]- |container_eddyqc_fix U:2 ?:5 ✗|
$ cd ~/data/BATMAN/Temp/

[02:40 PM]-[robertes@9520l-003953-l]-[~/.../BATMAN/Temp]-
$ docker run -it --rm -v $(pwd):/data mrtrix3:eddyqcfix dwifslpreproc /data/dwi_den_unr.mif /data/testeddyqc.mif -pe_dir ap -rpe_none -eddyqc_all /data/testeddyqc/
dwifslpreproc: 
dwifslpreproc: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
dwifslpreproc: 
dwifslpreproc: Generated scratch directory: /dwifslpreproc-tmp-V5EAJ1/
Command:  mrconvert /data/dwi_den_unr.mif /dwifslpreproc-tmp-V5EAJ1/dwi.mif -json_export /dwifslpreproc-tmp-V5EAJ1/dwi.json
dwifslpreproc: Changing to scratch directory (/dwifslpreproc-tmp-V5EAJ1/)
Command:  dirstat dwi.mif -output asym
dwifslpreproc: [WARNING] sampling of b=1000 shell is moderately asymmetric; distortion correction may benefit from use of: -eddy_options " ... --slm=linear ... "
dwifslpreproc: [WARNING] sampling of b=3000 shell is moderately asymmetric; distortion correction may benefit from use of: -eddy_options " ... --slm=linear ... "
Command:  mrinfo dwi.mif -export_grad_mrtrix grad.b
Command:  dwi2mask dwi.mif - | maskfilter - dilate - | mrconvert - eddy_mask.nii -datatype float32 -strides -1,+2,+3
Command:  mrconvert dwi.mif eddy_in.nii -strides -1,+2,+3,+4 -export_grad_fsl bvecs bvals -export_pe_eddy eddy_config.txt eddy_indices.txt
Command:  eddy_cuda10.2 --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --out=dwi_post_eddy --verbose
dwifslpreproc: CUDA version of 'eddy' was not successful; attempting OpenMP version
Command:  eddy_cpu --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --out=dwi_post_eddy --verbose
Command:  eddy_quad dwi_post_eddy -idx eddy_indices.txt -par eddy_config.txt -b bvals -m eddy_mask.nii
Command:  mrconvert dwi_post_eddy.nii.gz result.mif -strides -2,-3,-4,1 -fslgrad dwi_post_eddy.eddy_rotated_bvecs bvals
Function: os.makedirs('/data/testeddyqc')
Function: shutil.copy('dwi_post_eddy.eddy_parameters', '/data/testeddyqc/eddy_parameters')
Function: shutil.copy('dwi_post_eddy.eddy_movement_rms', '/data/testeddyqc/eddy_movement_rms')
Function: shutil.copy('dwi_post_eddy.eddy_restricted_movement_rms', '/data/testeddyqc/eddy_restricted_movement_rms')
Function: shutil.copy('dwi_post_eddy.eddy_post_eddy_shell_alignment_parameters', '/data/testeddyqc/eddy_post_eddy_shell_alignment_parameters')
Function: shutil.copy('dwi_post_eddy.eddy_post_eddy_shell_PE_translation_parameters', '/data/testeddyqc/eddy_post_eddy_shell_PE_translation_parameters')
Function: shutil.copy('dwi_post_eddy.eddy_outlier_report', '/data/testeddyqc/eddy_outlier_report')
Function: shutil.copy('dwi_post_eddy.eddy_outlier_map', '/data/testeddyqc/eddy_outlier_map')
Function: shutil.copy('dwi_post_eddy.eddy_outlier_n_stdev_map', '/data/testeddyqc/eddy_outlier_n_stdev_map')
Function: shutil.copy('dwi_post_eddy.eddy_outlier_n_sqr_stdev_map', '/data/testeddyqc/eddy_outlier_n_sqr_stdev_map')
Function: shutil.copytree('dwi_post_eddy.qc', '/data/testeddyqc/quad')
Function: shutil.copy('eddy_mask.nii', '/data/testeddyqc/eddy_mask.nii')
Command:  mrconvert result.mif /data/testeddyqc.mif
dwifslpreproc: Changing back to original directory (/)
dwifslpreproc: Deleting scratch directory (/dwifslpreproc-tmp-V5EAJ1/)

[02:55 PM]-[robertes@9520l-003953-l]-[~/.../BATMAN/Temp]-
$ ls testeddyqc/quad/
avg_b0.png  avg_b1999.png  avg_b3000.png  avg_b999.png  qc.json  qc.pdf  ref_list.png  ref.txt