Skip to content

Commit

Permalink
Merge pull request #957 from oesteban/enh/output-aseg
Browse files Browse the repository at this point in the history 
[ENH] Output aseg and aparc in T1w and BOLD spaces
  • Loading branch information
@oesteban
oesteban authored Feb 14, 2018
2 parents 3f86345 + 8c9ba29 commit 3b69fba
Show file tree
Hide file tree
Showing 6 changed files with 249 additions and 141 deletions.
6 changes: 6 additions & 0 deletions .circleci/ds005_outputs.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,8 @@ fmriprep/sub-01/anat/sub-01_T1w_class-WM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_dtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_inflated.L.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_inflated.R.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_label-aparcaseg_roi.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_label-aseg_roi.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_midthickness.L.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_midthickness.R.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_pial.L.surf.gii
Expand Down Expand Up @@ -48,6 +50,8 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin20
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_variant-smoothAROMAnonaggr_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_label-aparcaseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_label-aseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_AROMAnoiseICs.csv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_confounds.tsv
Expand All @@ -58,6 +62,8 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-MNI152NLin20
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-MNI152NLin2009cAsym_variant-smoothAROMAnonaggr_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-T1w_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-T1w_label-aparcaseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-T1w_label-aseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-T1w_preproc.nii.gz
fmriprep/sub-01.html
/tmp/ds005/derivatives
2 changes: 1 addition & 1 deletion docs/workflows.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -210,7 +210,7 @@ Based on the tissue segmentation of FreeSurfer (located in ``mri/aseg.mgz``)
and only when the :ref:`Surface Processing <workflows_surface>` step has been
executed, FMRIPREP replaces the brain mask with a refined one that derives
from the ``aseg.mgz`` file as described in
:mod:`fmriprep.workflows.anatomical.init_refine_brainmask_wf`.
:mod:`fmriprep.interfaces.freesurfer.grow_mask`.


BOLD preprocessing
Expand Down
166 changes: 106 additions & 60 deletions fmriprep/workflows/anatomical.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,6 @@
.. autofunction:: init_anat_preproc_wf
.. autofunction:: init_skullstrip_ants_wf
.. autofunction:: init_refine_brainmask_wf
Surface preprocessing
+++++++++++++++++++++
Expand Down Expand Up @@ -184,7 +183,7 @@ def init_anat_preproc_wf(skull_strip_template, output_spaces, template, debug,
'mni_mask', 'mni_seg', 'mni_tpms',
'template_transforms',
'subjects_dir', 'subject_id', 't1_2_fsnative_forward_transform',
't1_2_fsnative_reverse_transform', 'surfaces']),
't1_2_fsnative_reverse_transform', 'surfaces', 't1_aseg', 't1_aparc']),
name='outputnode')

buffernode = pe.Node(niu.IdentityInterface(
Expand Down Expand Up @@ -234,7 +233,9 @@ def init_anat_preproc_wf(skull_strip_template, output_spaces, template, debug,
('outputnode.subject_id', 'subject_id'),
('outputnode.t1_2_fsnative_forward_transform', 't1_2_fsnative_forward_transform'),
('outputnode.t1_2_fsnative_reverse_transform', 't1_2_fsnative_reverse_transform'),
('outputnode.surfaces', 'surfaces')]),
('outputnode.surfaces', 'surfaces'),
('outputnode.out_aseg', 't1_aseg'),
('outputnode.out_aparc', 't1_aparc')]),
(applyrefined, buffernode, [('out_file', 't1_brain')]),
(surface_recon_wf, buffernode, [
('outputnode.out_brainmask', 't1_mask')]),
Expand Down Expand Up @@ -336,7 +337,7 @@ def init_anat_preproc_wf(skull_strip_template, output_spaces, template, debug,
if freesurfer:
workflow.connect([
(surface_recon_wf, anat_reports_wf, [
('outputnode.out_report', 'inputnode.recon_report')])
('outputnode.out_report', 'inputnode.recon_report')]),
])
if 'template' in output_spaces:
workflow.connect([
Expand Down Expand Up @@ -368,6 +369,14 @@ def init_anat_preproc_wf(skull_strip_template, output_spaces, template, debug,
]),
])

if freesurfer:
workflow.connect([
(surface_recon_wf, anat_derivatives_wf, [
('outputnode.out_aseg', 'inputnode.t1_fs_aseg'),
('outputnode.out_aparc', 'inputnode.t1_fs_aparc'),
]),
])

return workflow


Expand Down Expand Up @@ -608,6 +617,37 @@ def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):
-noskullstrip
The second phase imports an externally computed skull-stripping mask.
This workflow refines the external brainmask using the internal mask
implicit the the FreeSurfer's ``aseg.mgz`` segmentation,
to reconcile ANTs' and FreeSurfer's brain masks.
First, the ``aseg.mgz`` mask from FreeSurfer is refined in two
steps, using binary morphological operations:
1. With a binary closing operation the sulci are included
into the mask. This results in a smoother brain mask
that does not exclude deep, wide sulci.
2. Fill any holes (typically, there could be a hole next to
the pineal gland and the corpora quadrigemina if the great
cerebral brain is segmented out).
Second, the brain mask is grown, including pixels that have a high likelihood
to the GM tissue distribution:
3. Dilate and substract the brain mask, defining the region to search for candidate
pixels that likely belong to cortical GM.
4. Pixels found in the search region that are labeled as GM by ANTs
(during ``antsBrainExtraction.sh``) are directly added to the new mask.
5. Otherwise, estimate GM tissue parameters locally in patches of ``ww`` size,
and test the likelihood of the pixel to belong in the GM distribution.
This procedure is inspired on mindboggle's solution to the problem:
https://github.com/nipy/mindboggle/blob/7f91faaa7664d820fe12ccc52ebaf21d679795e2/mindboggle/guts/segment.py#L1660
The final phase resumes reconstruction, using the T2w image to assist
in finding the pial surface, if available.
See :py:func:`~fmriprep.workflows.anatomical.init_autorecon_resume_wf` for details.
Expand Down Expand Up @@ -666,6 +706,10 @@ def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):
midthickness (or graymid) surface, and inflated surfaces
out_brainmask
Refined brainmask, derived from FreeSurfer's ``aseg`` volume
out_aseg
FreeSurfer's aseg segmentation, in native T1w space
out_aparc
FreeSurfer's aparc+aseg segmentation, in native T1w space
out_report
Reportlet visualizing quality of surface alignment
Expand All @@ -685,7 +729,7 @@ def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):
niu.IdentityInterface(
fields=['subjects_dir', 'subject_id', 't1_2_fsnative_forward_transform',
't1_2_fsnative_reverse_transform', 'surfaces', 'out_brainmask',
'out_report']),
'out_aseg', 'out_aparc', 'out_report']),
name='outputnode')

recon_config = pe.Node(FSDetectInputs(hires_enabled=hires), name='recon_config')
Expand All @@ -704,7 +748,10 @@ def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):

autorecon_resume_wf = init_autorecon_resume_wf(omp_nthreads=omp_nthreads)
gifti_surface_wf = init_gifti_surface_wf()
refine_brainmask_wf = init_refine_brainmask_wf()

aseg_to_native_wf = init_segs_to_native_wf()
aparc_to_native_wf = init_segs_to_native_wf(segmentation='aparc_aseg')
refine = pe.Node(RefineBrainMask(), name='refine')

workflow.connect([
# Configuration
Expand Down Expand Up @@ -736,19 +783,28 @@ def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):
('out_reg_file', 'inputnode.t1_2_fsnative_reverse_transform')]),
(fsnative_2_t1_xfm, t1_2_fsnative_xfm, [('out_reg_file', 'in_lta')]),
# Refine ANTs mask, deriving new mask from FS' aseg
(inputnode, refine_brainmask_wf, [('corrected_t1', 'inputnode.in_file'),
('ants_segs', 'inputnode.ants_segs')]),
(autorecon_resume_wf, refine_brainmask_wf, [
(inputnode, refine, [('corrected_t1', 'in_anat'),
('ants_segs', 'in_ants')]),
(inputnode, aseg_to_native_wf, [('corrected_t1', 'inputnode.in_file')]),
(autorecon_resume_wf, aseg_to_native_wf, [
('outputnode.subjects_dir', 'inputnode.subjects_dir'),
('outputnode.subject_id', 'inputnode.subject_id')]),
(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')]),
(aseg_to_native_wf, refine, [('outputnode.out_file', 'in_aseg')]),

# Output
(autorecon_resume_wf, outputnode, [('outputnode.subjects_dir', 'subjects_dir'),
('outputnode.subject_id', 'subject_id'),
('outputnode.out_report', 'out_report')]),
(gifti_surface_wf, outputnode, [('outputnode.surfaces', 'surfaces')]),
(t1_2_fsnative_xfm, outputnode, [('out_lta', 't1_2_fsnative_forward_transform')]),
(fsnative_2_t1_xfm, outputnode, [('out_reg_file', 't1_2_fsnative_reverse_transform')]),
(refine_brainmask_wf, outputnode, [('outputnode.out_file', 'out_brainmask')]),
(refine, outputnode, [('out_file', 'out_brainmask')]),
(aseg_to_native_wf, outputnode, [('outputnode.out_file', 'out_aseg')]),
(aparc_to_native_wf, outputnode, [('outputnode.out_file', 'out_aparc')]),
])

return workflow
Expand Down Expand Up @@ -955,52 +1011,27 @@ def init_gifti_surface_wf(name='gifti_surface_wf'):
return workflow


def init_refine_brainmask_wf(name='refine_brainmask'):
def init_segs_to_native_wf(name='segs_to_native', segmentation='aseg'):
"""
This workflow refines the brainmask implicit in the FreeSurfer's ``aseg.mgz``
brain tissue segmentation to reconcile ANTs' and FreeSurfer's brain masks.
First, the ``aseg.mgz`` mask from FreeSurfer is refined in two
steps, using binary morphological operations:
1. With a binary closing operation the sulci are included
into the mask. This results in a smoother brain mask
that does not exclude deep, wide sulci.
2. Fill any holes (typically, there could be a hole next to
the pineal gland and the corpora quadrigemina if the great
cerebral brain is segmented out).
Second, the brain mask is grown, including pixels that have a high likelihood
to the GM tissue distribution:
3. Dilate and substract the brain mask, defining the region to search for candidate
pixels that likely belong to cortical GM.
4. Pixels found in the search region that are labeled as GM by ANTs
(during ``antsBrainExtraction.sh``) are directly added to the new mask.
5. Otherwise, estimate GM tissue parameters locally in patches of ``ww`` size,
and test the likelihood of the pixel to belong in the GM distribution.
This procedure is inspired on mindboggle's solution to the problem:
https://github.com/nipy/mindboggle/blob/master/mindboggle/guts/segment.py#L1660
Get a segmentation from FreeSurfer conformed space into native T1w space
.. workflow::
:graph2use: orig
:simple_form: yes
from fmriprep.workflows.anatomical import init_refine_brainmask_wf
wf = init_refine_brainmask_wf()
from fmriprep.workflows.anatomical import init_segs_to_native_wf
wf = init_segs_to_native_wf()
**Parameters**
segmentation
The name of a segmentation ('aseg' or 'aparc_aseg' or 'wmparc')
**Inputs**
in_file
Anatomical, merged T1w image after INU correction
ants_segs
Brain tissue segmentation from ANTS ``antsBrainExtraction.sh``
subjects_dir
FreeSurfer SUBJECTS_DIR
subject_id
Expand All @@ -1010,33 +1041,37 @@ def init_refine_brainmask_wf(name='refine_brainmask'):
**Outputs**
out_file
New, refined brain mask
The selected segmentation, after resampling in native space
"""
workflow = pe.Workflow(name=name)

workflow = pe.Workflow(name='%s_%s' % (name, segmentation))
inputnode = pe.Node(niu.IdentityInterface([
'in_file', 'ants_segs', 'subjects_dir', 'subject_id']), name='inputnode')
'in_file', 'subjects_dir', 'subject_id']), name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(['out_file']), name='outputnode')
get_aseg = pe.Node(nio.FreeSurferSource(), name='get_aseg')
# 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')
refine = pe.Node(RefineBrainMask(), name='refine')

if segmentation.startswith('aparc'):
if segmentation == 'aparc_aseg':
def _sel(x): return x[0]
elif segmentation == 'aparc_a2009s':
def _sel(x): return x[1]
elif segmentation == 'aparc_dkt':
def _sel(x): return x[2]
segmentation = (segmentation, _sel)

workflow.connect([
(inputnode, refine, [('in_file', 'in_anat'),
('ants_segs', 'in_ants')]),
(inputnode, get_aseg, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
(inputnode, fssource, [
('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
(inputnode, tonii, [('in_file', 'reslice_like')]),
(get_aseg, tonative, [('aseg', 'seg_file'),
(fssource, tonative, [(segmentation, 'seg_file'),
('rawavg', 'template_file'),
('aseg', 'reg_header')]),
(tonative, tonii, [('vol_label_file', 'in_file')]),
(tonii, refine, [('out_file', 'in_aseg')]),
(refine, outputnode, [('out_file', 'out_file')]),
(tonii, outputnode, [('out_file', 'out_file')]),
])

return workflow


Expand Down Expand Up @@ -1103,7 +1138,8 @@ def init_anat_derivatives_wf(output_dir, output_spaces, template, freesurfer,
't1_preproc', 't1_mask', 't1_seg', 't1_tpms',
't1_2_mni_forward_transform', 't1_2_mni_reverse_transform',
't1_2_mni', 'mni_mask', 'mni_seg', 'mni_tpms',
't1_2_fsnative_forward_transform', 'surfaces']),
't1_2_fsnative_forward_transform', 'surfaces',
't1_fs_aseg', 't1_fs_aparc']),
name='inputnode')

t1_name = pe.Node(niu.Function(function=fix_multi_T1w_source_name), name='t1_name')
Expand Down Expand Up @@ -1196,6 +1232,12 @@ def init_anat_derivatives_wf(output_dir, output_spaces, template, freesurfer,
])

if freesurfer:
ds_t1_fsaseg = pe.Node(
DerivativesDataSink(base_directory=output_dir, suffix='label-aseg_roi'),
name='ds_t1_fsaseg', run_without_submitting=True)
ds_t1_fsparc = pe.Node(
DerivativesDataSink(base_directory=output_dir, suffix='label-aparcaseg_roi'),
name='ds_t1_fsparc', run_without_submitting=True)
workflow.connect([
(inputnode, lta_2_itk, [('t1_2_fsnative_forward_transform', 'in_lta')]),
(t1_name, ds_t1_fsnative, [('out', 'source_file')]),
Expand All @@ -1204,6 +1246,10 @@ def init_anat_derivatives_wf(output_dir, output_spaces, template, freesurfer,
(inputnode, ds_surfs, [('surfaces', 'in_file')]),
(t1_name, ds_surfs, [('out', 'source_file')]),
(name_surfs, ds_surfs, [('out_name', 'suffix')]),
(inputnode, ds_t1_fsaseg, [('t1_fs_aseg', 'in_file')]),
(inputnode, ds_t1_fsparc, [('t1_fs_aparc', 'in_file')]),
(t1_name, ds_t1_fsaseg, [('out', 'source_file')]),
(t1_name, ds_t1_fsparc, [('out', 'source_file')]),
])
if 'template' in output_spaces:
workflow.connect([
Expand Down
2 changes: 2 additions & 0 deletions fmriprep/workflows/base.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -449,6 +449,8 @@ def init_single_subject_wf(subject_id, task_id, name,
('outputnode.t1_brain', 'inputnode.t1_brain'),
('outputnode.t1_mask', 'inputnode.t1_mask'),
('outputnode.t1_seg', 'inputnode.t1_seg'),
('outputnode.t1_aseg', 'inputnode.t1_aseg'),
('outputnode.t1_aparc', 'inputnode.t1_aparc'),
('outputnode.t1_tpms', 'inputnode.t1_tpms'),
('outputnode.t1_2_mni_forward_transform', 'inputnode.t1_2_mni_forward_transform'),
('outputnode.t1_2_mni_reverse_transform', 'inputnode.t1_2_mni_reverse_transform'),
Expand Down
Loading

0 comments on commit 3b69fba

Please sign in to comment.