[ENH] Template-based masking of EPI boldrefs #1321

oesteban · 2018-10-15T18:49:01Z

Changes proposed in this pull request

This PR explores template-based masking of boldrefs to initialize the skull-stripping workflow (see issues related on #1000).

This PR is also highly related to #1050.

Documentation that should be reviewed

This is WIP, will update documentation when it is proven to work out.

oesteban · 2018-10-15T23:12:26Z

So these are the results:

I still need to investigate what happened here: https://2488-53608443-gh.circle-artifacts.com/0/tmp/data/reports/ds000216/sub-03_task-rest_echo-1_bold_masks.svg

oesteban · 2018-10-15T23:15:12Z

The problem with echo 1 of ds216 seems to have been introduced here (this PR vs latest master)

oesteban · 2018-10-16T04:22:03Z

The weird result in https://2488-53608443-gh.circle-artifacts.com/0/tmp/data/reports/ds000216/sub-03_task-rest_echo-1_bold_masks.svg does not happen when I test locally (???)

oesteban · 2018-10-16T14:32:58Z

Seems like the weird problem on ds216 is now fixed. At this point I would ask: do you think it is maybe worth changing the whole algorithm to the following?:

Initialization: ANTs' AI, using the template as target and the boldref as moving
Gross mask, applyTransform on the inverted transform of 1)
N4 on the boldref with the gross mask
First registration: very fast refinement (Rigid) of the gross mask using the template as target and the boldref as moving and initialized with 1)
N4 on the boldref with the less-gross mask
Second registration (Affine) initialized with 4)
Remaining boldref refinement with the final mask

effigies · 2018-10-16T16:18:08Z

Let's test on the subject from #1181, as well.

oesteban · 2018-10-16T23:59:18Z

Still testing on additional datasets, but this seems ready for review.
Artifacts in the latest commit without [skip ci] -> https://circleci.com/gh/oesteban/fmriprep/2525#artifacts/containers/0

Refs. #1000, #1050, #1321. Also includes a new filter of branches so builds other than tests are skipped if the name of the branch starts with ``tests?/``.

zhifangy · 2018-10-18T03:24:02Z

Hi, @oesteban. I did a quick test using this PR on my previous failed data. Generally, it gives pretty good results. But I think there are several issues we need to address.

The pre_mask's header should be fixed before N4 correction. I encountered Inputs do not occupy the same physical space! error on one of my test image.
The N4 correction has no effect on some of the unwrapped images (eg. sub-26 rest) in bold_bold_trans_wf. I tried to run N4 correction manually on the ref_image_valid.nii.gz and it yielded the same incorrect result.
What if the BOLD image only covers part of brain volume? I think the initial affine transformation would generate a quite large mask for N4 correction. I think we should include some partial volume scan (especially for scans only covers 30-40 slices parallels to the long axis of hippocampus) in the test battery to see how well the method works.

oesteban · 2018-10-18T16:16:01Z

Thanks a lot for your precious feedback! @ZhifangYe

The pre_mask's header should be fixed before N4 correction. I encountered Inputs do not occupy the same physical space! error on one of my test image.

Could you provide more information about the error (full trace) or even the dataset (privately is fine) where this is happening? This is a new caching procedure we are testing and it does not surprise me you got this kind of problem.

The N4 correction has no effect on some of the unwrapped images (eg. sub-26 rest) in bold_bold_trans_wf. I tried to run N4 correction manually on the ref_image_valid.nii.gz and it yielded the same incorrect result.

Cool, sub-26_task-rest is now within the regression tests, so I'll work on this one particularly.

What if the BOLD image only covers part of brain volume? I think the initial affine transformation would generate a quite large mask for N4 correction. I think we should include some partial volume scan (especially for scans only covers 30-40 slices parallels to the long axis of hippocampus) in the test battery to see how well the method works.

This question is also very pertinent. I'll dig up some partial FoV datasets from OpenNeuro and add them to the test battery.

Thanks a lot for your input, very much appreciated!

oesteban · 2018-10-19T04:17:13Z

Fixes #1000
Fixes #1181

oesteban · 2018-10-19T04:36:31Z

Ref #900

zhifangy · 2018-10-19T05:58:10Z

Here's the fMRIprep error log and the verbose log of N4 correction command.

I think it's due to the very small discrepancy between the qform matrix of pre_mask and ref_image.

The following link is the raw data to replicate this error. https://www.dropbox.com/s/akfyadrih5lgcbd/sub-30.zip?dl=0

oesteban · 2018-10-24T16:58:36Z

I think it's due to the very small discrepancy between the qform matrix of pre_mask and ref_image

Correct, there is a minimal difference in the qform.

oesteban · 2018-10-24T18:11:24Z

Alright, this ready for review (@ZhifangYe, @effigies). I've just fixed the issue of mismatched headers before N4.

Since we don't make any promises about very limited FoV (https://github.com/poldracklab/fmriprep/labels/partial%20FOV), I propose to merge this in and come back later to the FoV issue.

Regarding sub-26_task-rest, please check out the regression tests under the test_pytest build of Circle.

effigies

I'm not sure about the new interface.

effigies · 2018-10-24T18:17:52Z

fmriprep/interfaces/images.py

+        imghdr['dim_info'] = refhdr['dim_info']  # dim_info is lost sometimes
+
+        # Set qform
+        qform, qcode = refhdr.get_qform(coded=True)


Are all images guaranteed to have non-zero codes? If qcode == 0, qform == None.

https://github.com/nipy/nibabel/blob/d5494f3350967b65bd6de1abefd95ab2899044e0/nibabel/nifti1.py#L916-L917

effigies · 2018-10-24T18:18:29Z

fmriprep/interfaces/images.py

+        imghdr.set_qform(qform, int(qcode))
+
+        # Set sform
+        sform, scode = refhdr.get_sform(coded=True)


Also the case for sforms:

https://github.com/nipy/nibabel/blob/d5494f3350967b65bd6de1abefd95ab2899044e0/nibabel/nifti1.py#L1059-L1060

effigies · 2018-10-24T18:24:00Z

fmriprep/interfaces/images.py

+                                   newpath=runtime.cwd)
+
+        imgnii.__class__(imgnii.get_data(), imgnii.affine, imghdr).to_filename(
+            out_file)


I don't think this will work how you want. You may want to add tests.

If imgnii.affine does not match the result of imgnii.header.get_best_affine(), it will be pushed into the header, probably as the sform. If you've just put refhdr.get_sform() into the imghdr sform matrix, then these are unlikely to match, and you'll be pushing the original affine right back in.

A better approach would be:

imgnii.__class__(imgnii.get_data(), imghdr.get_best_affine(), imghdr).to_filename( out_file)

oesteban · 2018-10-24T22:57:47Z

This is sub-26_task-rest: https://2591-53608443-gh.circle-artifacts.com/0/tmp/data/reports/ds001240/sub-26_task-rest_bold_masks.svg which looks okay.

We are seeing ds005 fail due to a problem checking filenames that is also happening in master. I'm guessing that would be a trivial change to do in master.

Thumbs up?

oesteban · 2018-10-25T00:36:09Z

ds005 problems addressed here - #1344

If there are no further comments or voices against, I'll be merging later today and close #1050 as this PR supersedes that one.

Thanks to @ZhifangYe, this PR has been only possible with all the new data we have now for regression tests.

effigies

This looks good. I took another read through, and only saw one thing, which should have no impact one way or another, but would reduce the number of branches.

effigies · 2018-10-24T23:19:25Z

fmriprep/workflows/bold/util.py

+    if pre_mask:
+        workflow.connect([
+            (inputnode, enhance_and_skullstrip_bold_wf, [('bold_mask', 'inputnode.pre_mask')]),
+        ])


I think this should be okay to set unconditionally.

zhifangy

The test results look good to me. I'm really happy to see the issue is resolved. 👍

I read through the code and only find the doc in init_enhance_and_skullstrip_bold_wf line 185 doesn't match. I think it should be '7. Calculate a final mask as the intersection of 4) and 6).'.

[ENH] Template-based masking of EPI boldrefs

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oesteban mentioned this pull request Oct 15, 2018

[ENH] Add "fMRIPrep" template, with new boldref template nipreps/niworkflows#255

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oesteban added 3 commits October 15, 2018 11:52

fix flake8 error

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use nipreps/niworkflows@0946bad

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update pinning to release

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oesteban added 3 commits October 15, 2018 23:09

new registration parameters

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pre-cache template getter

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fix ds005 problem

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oesteban mentioned this pull request Oct 16, 2018

[ENH/WIP] Robust EPI Mask for heavily nonuniform image #1050

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oesteban added 2 commits October 16, 2018 12:46

1) shorten registration; 2) accept a pre_mask

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[skip ci] update documentation

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oesteban changed the title ~~[ENH,WIP] Template-based masking of EPI boldrefs~~ [ENH] Template-based masking of EPI boldrefs Oct 16, 2018

oesteban added 3 commits October 17, 2018 00:23

Merge remote-tracking branch 'upstream/master' into fix/1000

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Merge branch 'hotfix/reports-3' into fix/1000

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Merge branch 'hotfix/reports-3' into fix/1000

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oesteban added a commit that referenced this pull request Oct 17, 2018

[TST] Add heavily-nonuniform boldrefs for regression tests

6215779

Refs. #1000, #1050, #1321. Also includes a new filter of branches so builds other than tests are skipped if the name of the branch starts with ``tests?/``.

oesteban mentioned this pull request Oct 17, 2018

[TST] Add heavily-nonuniform boldrefs for regression tests #1329

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Merge remote-tracking branch 'upstream/master' into fix/1000

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Merge remote-tracking branch 'upstream/master' into fix/1000

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fix header mismatch problem

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[skip ci] Pin niworkflows==0.4.4

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effigies reviewed Oct 24, 2018

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address @effigies' comments on MatchHeader

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fix master

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effigies approved these changes Oct 25, 2018

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effigies added this to the 1.2.0 milestone Oct 25, 2018

oesteban added 2 commits October 24, 2018 18:07

Merge branch 'ds005/expected-outputs' into fix/1000

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remove one branch

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zhifangy approved these changes Oct 25, 2018

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[skip ci] fix minimal error in docs

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oesteban merged commit 874c4ce into nipreps:master Oct 25, 2018

oesteban deleted the fix/1000 branch October 25, 2018 03:39

oesteban mentioned this pull request Oct 27, 2018

Reference brainmask failing for highly intensity nonuniform bold data #1000

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[ENH] Template-based masking of EPI boldrefs #1321

[ENH] Template-based masking of EPI boldrefs #1321

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[ENH] Template-based masking of EPI boldrefs #1321

[ENH] Template-based masking of EPI boldrefs #1321

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oesteban commented Oct 15, 2018

Changes proposed in this pull request

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