FIX: Use t1w2fsnative_xfm to resample segmentations

[effigies]

Closes #154.

As noted in #154, if fsnative is not pre-aligned with the T1w template fMRIPrep produces, aparc/aseg do not get properly aligned, and due to using FreeSurfer outputs to refine the brainmask, everything suffers.

This first pipes the t1w2fsnative_xfm to the segmentation workflows (init_segs_to_native_wf). This workflow had used mri_label2vol + mri_convert. The mri_label2vol was already converting to NIfTI, so I dropped mri_convert.

I manually confirmed that using mri_label2vol with the inverse LTA gets the alignment right.

I also noticed that mri_label2vol has label, annotation and volume modes. Since aseg.mgz and aparc+aseg.mgz are already volumes (.mgz, rather than .label or .annot), I checked whether mri_vol2vol could be used.

That also worked. Even better, it takes its transforms in the usual direction (source -> target), so we don't have to leave comments about why we either pass the inverted LTA file, or pass the normal file and an "invert" flag.

Because the interface changed, I changed the name of the node.

---

Bug-fix status: This changes the workflow, but it does so in a way that should keep working directories reusable. And it fixes a bug in several versions of fMRIPrep. So I would suggest that we make an exception and release this as a bug-fix, which will allow us to fix the 20.0 and 20.1 series (and backport to 1.5, if it ever comes up).

[oesteban]

This looks great.

Maybe it's going to be easier to change the base to maint/20.0.x to avoid the license problem. Then progress changes to 20.1 and master (and backport if we get on a commitment strike).

[oesteban]

Okay it was late when I reviewed this and I was probably unclear on my suggestion. What I meant with the PR base is:

• Can you base the PR on maint/0.5.x?
• We release a bugfix on sMRIPrep-0.5.x and also fMRIPrep-20.0.x
• We figure out the canary problem elsewhere
• We port to maint/0.6.x and master.

[effigies]

maint/0.5.x can be safely merged into maint/0.6.x.

Diff:

diff --git a/.circleci/config.yml b/.circleci/config.yml
index ba2167709..09d304ca7 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -249,7 +249,8 @@ jobs:
             pyenv local $PY2
             echo -n "Python version: "
             python --version
-            pip install --upgrade pip setuptools
+            pip install --upgrade "pip<21"
+            pip install --upgrade setuptools
             pip install --upgrade wrapper/
             which smriprep-docker
             smriprep-docker -i poldracklab/smriprep:latest --help
diff --git a/smriprep/workflows/surfaces.py b/smriprep/workflows/surfaces.py
index 9e6702323..cd77b1536 100644
--- a/smriprep/workflows/surfaces.py
+++ b/smriprep/workflows/surfaces.py
@@ -231,10 +231,12 @@ gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].
         (autorecon_resume_wf, aseg_to_native_wf, [
             ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
             ('outputnode.subject_id', 'inputnode.subject_id')]),
+        (fsnative2t1w_xfm, aseg_to_native_wf, [('out_reg_file', 'inputnode.fsnative2t1w_xfm')]),
         (inputnode, aparc_to_native_wf, [('corrected_t1', 'inputnode.in_file')]),
         (autorecon_resume_wf, aparc_to_native_wf, [
             ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
             ('outputnode.subject_id', 'inputnode.subject_id')]),
+        (fsnative2t1w_xfm, aparc_to_native_wf, [('out_reg_file', 'inputnode.fsnative2t1w_xfm')]),
         (aseg_to_native_wf, refine, [('outputnode.out_file', 'in_aseg')]),
 
         # Output
@@ -502,6 +504,8 @@ def init_segs_to_native_wf(name='segs_to_native', segmentation='aseg'):
         FreeSurfer SUBJECTS_DIR
     subject_id
         FreeSurfer subject ID
+    fsnative2t1w_xfm
+        LTA-style affine matrix translating from FreeSurfer-conformed subject space to T1w
 
     Outputs
     -------
@@ -510,13 +514,15 @@ def init_segs_to_native_wf(name='segs_to_native', segmentation='aseg'):
 
     """
     workflow = Workflow(name='%s_%s' % (name, segmentation))
-    inputnode = pe.Node(niu.IdentityInterface([
-        'in_file', 'subjects_dir', 'subject_id']), name='inputnode')
+    inputnode = pe.Node(
+        niu.IdentityInterface(['in_file', 'subjects_dir', 'subject_id', 'fsnative2t1w_xfm']),
+        name='inputnode')
     outputnode = pe.Node(niu.IdentityInterface(['out_file']), name='outputnode')
     # Extract the aseg and aparc+aseg outputs
     fssource = pe.Node(nio.FreeSurferSource(), name='fs_datasource')
-    tonative = pe.Node(fs.Label2Vol(), name='tonative')
-    tonii = pe.Node(fs.MRIConvert(out_type='niigz', resample_type='nearest'), name='tonii')
+    # Resample from T1.mgz to T1w.nii.gz, applying any offset in fsnative2t1w_xfm,
+    # and convert to NIfTI while we're at it
+    resample = pe.Node(fs.ApplyVolTransform(transformed_file='seg.nii.gz'), name='resample')
 
     if segmentation.startswith('aparc'):
         if segmentation == 'aparc_aseg':
@@ -531,12 +537,10 @@ def init_segs_to_native_wf(name='segs_to_native', segmentation='aseg'):
         (inputnode, fssource, [
             ('subjects_dir', 'subjects_dir'),
             ('subject_id', 'subject_id')]),
-        (inputnode, tonii, [('in_file', 'reslice_like')]),
-        (fssource, tonative, [(segmentation, 'seg_file'),
-                              ('rawavg', 'template_file'),
-                              ('aseg', 'reg_header')]),
-        (tonative, tonii, [('vol_label_file', 'in_file')]),
-        (tonii, outputnode, [('out_file', 'out_file')]),
+        (inputnode, resample, [('in_file', 'target_file'),
+                               ('fsnative2t1w_xfm', 'lta_file')]),
+        (fssource, resample, [(segmentation, 'source_file')]),
+        (resample, outputnode, [('transformed_file', 'out_file')]),
     ])
     return workflow

[mgxd]

@effigies does this also close #200?

[effigies]

No.