[FIX] return non-enhanced volumes from dwi_flirt

[jdkent]

Fixes #1787

Changes proposed in this pull request

• applies the matrix transforms from the adjusted/enhanced non-B0 volumes to the original non-B0 volumes, so that the image intensities remain the same. Ideally flirt should just estimate/apply linear transforms, not change the image intensities. As @salma1601 mentioned, exposure.equalize_adapthist appears to be the culprit.

example dwi data for testing

related code that can be used for testing (with modification)

[codecov-io]

Codecov Report

Merging #2547 into master will increase coverage by <.01%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #2547      +/-   ##
==========================================
+ Coverage   67.04%   67.04%   +<.01%     
==========================================
  Files         332      332              
  Lines       42511    42512       +1     
  Branches     5262     5262              
==========================================
+ Hits        28500    28501       +1     
  Misses      13315    13315              
  Partials      696      696

Flag	Coverage Δ
#smoketests	50.67% <ø> (ø)	⬆️
#unittests	64.34% <100%> (-0.04%)	⬇️

Impacted Files	Coverage Δ
nipype/workflows/dmri/fsl/utils.py	19.29% <100%> (+0.17%)	⬆️

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[PkuClosed]

Hi @jdkent

Thank you for the fix. I tried to revise utils.py as suggested here. However, I got some errors after running

dir_ecc = directory
ecc = ecc_pipeline()
ecc.inputs.inputnode.in_file = dwiname
ecc.inputs.inputnode.in_bval = bvalsname
ecc.inputs.inputnode.in_mask = output_mask_name
ecc.base_dir = dir_ecc
res_ecc = ecc.run()

The output log is too long, so I selected some output that might be helpful as follows

Subnode 89 failed
Error: Traceback (most recent call last):

File "/home/chuyangye/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/utils.py", line 106, in nodelist_runner
result = node.run(updatehash=updatehash)

File "/home/chuyangye/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 487, in run
result = self._run_interface(execute=True)

File "/home/chuyangye/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 571, in _run_interface
return self._run_command(execute)

File "/home/chuyangye/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 650, in _run_command
result = self._interface.run(cwd=outdir)

File "/home/chuyangye/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 516, in run
runtime = self._run_interface(runtime)

File "/home/chuyangye/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 1023, in _run_interface
self.raise_exception(runtime)

File "/home/chuyangye/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 960, in raise_exception
).format(**runtime.dictcopy()))

RuntimeError: Command:
flirt -in /home/HDD1/chuyangye/PD/data2mm/20180417/SE7/eddy_correct/DWICoregistration/SplitDWIs/vol0089.nii.gz -ref /home/HDD1/chuyangye/PD/data2mm/20180417/SE7/eddy_correct/DWICoregistration/B0Equalize/S
E7_NODDI-90_20180414161922_7_float_avg_b0_corrected_enh.nii.gz -out vol0089_flirt.nii.gz -omat vol0089_flirt.mat -applyxfm -setbackground 0.000000 -init /home/HDD1/chuyangye/PD/data2mm/20180417/SE7/eddy_c
orrect/DWICoregistration/CoRegistration/mapflow/_CoRegistration89/vol0089_enh_flirt.mat -interp spline
Standard output:

Standard error:
terminate called after throwing an instance of 'NEWMAT::SingularException'
Aborted (core dumped)
Return code: 134

180421-23:11:33,453 workflow INFO:
[Node] Setting-up "eddy_correct.GatherMatrices" in "/home/HDD1/chuyangye/PD/data2mm/20180417/SE7/eddy_correct/GatherMatrices".
180421-23:11:33,890 workflow INFO:
[Node] Running "GatherMatrices" ("nipype.interfaces.utility.wrappers.Function")
180421-23:11:34,645 workflow INFO:
[Node] Finished "eddy_correct.GatherMatrices".
180421-23:11:34,646 workflow INFO:
***********************************
180421-23:11:34,647 workflow ERROR:
could not run node: eddy_correct.DWICoregistration.ApplyXFMs
180421-23:11:34,647 workflow INFO:
crashfile: /home/chuyangye/crash-20180421-231133-chuyangye-ApplyXFMs-530c0c4a-fb9b-4b9e-a6ff-2c1900da036b.pklz
180421-23:11:34,647 workflow INFO:
***********************************

I am wondering if I missed anything in the fix.

Chuyang

[jdkent]

I'm not entirely sure what is causing the error, but a google search turned up this.

Thanks for posting the output, given with what we have, I think the next pertinent question is what version of FSL you are using? If it's 5.0.8 like the user in the fsl listserv is using that may be the culprit.

[effigies]

@oesteban this appears to be your contribution (#903), so I think you're probably best placed to review this. I know you've got a lot on your plate, but assigning you just to remind you when you get time.

Any others who feel comfortable reviewing should go ahead and do so.

[oesteban]

At a first sight, using spline interpolation here seems like a good idea but will introduce negative values. Thresholding after this step would be advisable

[jdkent]

Good catch, I didn't know that about spline. I'll add thresholding back in.

[effigies]

@oesteban It would be good to feature freeze 1.0.3 today so we can run final tests on Friday. Your call whether this goes in.

[oesteban]

Merged!