ENH: fsLR output space, cifti output in HCP grayordinate space #1887
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| Original file line number | Diff line number | Diff line change |
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@@ -412,7 +412,7 @@ def init_func_preproc_wf( | |
| outputnode = pe.Node(niu.IdentityInterface( | ||
| fields=['bold_t1', 'bold_t1_ref', 'bold_mask_t1', 'bold_aseg_t1', 'bold_aparc_t1', | ||
| 'bold_std', 'bold_std_ref', 'bold_mask_std', 'bold_aseg_std', 'bold_aparc_std', | ||
| 'bold_native', 'bold_cifti', 'cifti_variant', 'cifti_metadata', 'surfaces', | ||
| 'confounds', 'aroma_noise_ics', 'melodic_mix', 'nonaggr_denoised_file', | ||
| 'confounds_metadata']), | ||
| name='outputnode') | ||
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@@ -431,10 +431,11 @@ def init_func_preproc_wf( | |
| name='summary', mem_gb=DEFAULT_MEMORY_MIN_GB, run_without_submitting=True) | ||
| summary.inputs.dummy_scans = dummy_scans | ||
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| # CIFTI output | ||
| cifti_spaces = {'fsLR'} if 'fsLR' in output_spaces else \ | ||
| set(output_spaces.keys()).intersection(('fsaverage5', 'fsaverage6')) | ||
| fsaverage_den = output_spaces.get('fsaverage', {}).get('den') | ||
| if fsaverage_den and 'fsLR' not in cifti_spaces: | ||
| cifti_spaces.add(FSAVERAGE_DENSITY[fsaverage_den]) | ||
| cifti_output = cifti_output and cifti_spaces | ||
| func_derivatives_wf = init_func_derivatives_wf( | ||
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@@ -463,7 +464,7 @@ def init_func_preproc_wf( | |
| ('nonaggr_denoised_file', 'inputnode.nonaggr_denoised_file'), | ||
| ('bold_cifti', 'inputnode.bold_cifti'), | ||
| ('cifti_variant', 'inputnode.cifti_variant'), | ||
| ('cifti_metadata', 'inputnode.cifti_metadata'), | ||
| ('confounds_metadata', 'inputnode.confounds_metadata'), | ||
| ]), | ||
| ]) | ||
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@@ -923,10 +924,12 @@ def init_func_preproc_wf( | |
| # SURFACES ################################################################################## | ||
| surface_spaces = [space for space in output_spaces.keys() if space.startswith('fs')] | ||
| if freesurfer and surface_spaces: | ||
| fslr_density = output_spaces.get('fsLR', {}).get('den', '32k') | ||
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There was a problem hiding this comment. We'll need to address #1895 if we want this to work. There was a problem hiding this comment. i've opened nipreps/smriprep#145 - since that isn't exclusive to this I'll submit a fix separate from this. A quick workaround is to specify at least one parameter for |
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| LOGGER.log(25, 'Creating BOLD surface-sampling workflow.') | ||
| bold_surf_wf = init_bold_surf_wf(mem_gb=mem_gb['resampled'], | ||
| output_spaces=surface_spaces, | ||
| medial_surface_nan=medial_surface_nan, | ||
| fslr_density=fslr_density, | ||
| name='bold_surf_wf') | ||
| workflow.connect([ | ||
| (inputnode, bold_surf_wf, [ | ||
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@@ -944,26 +947,35 @@ def init_func_preproc_wf( | |
| *Grayordinates* files [@hcppipelines], which combine surface-sampled | ||
| data and volume-sampled data, were also generated. | ||
| """ | ||
| cifti_volume = "MNI152NLin6Asym" if 'fsLR' in cifti_spaces else "MNI152NLin2009cAsym" | ||
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There was a problem hiding this comment. I thought they used an FSL-packaged (and slightly weird) version of the template. Do we need to account for that? There was a problem hiding this comment. we are using the same labelled MNI template the HCP folks use to generate the CIFTIs, which should be in same space as the template - what do you mean by slightly weird? There was a problem hiding this comment. I might be misremembering. During the TemplateFlow changeover we switched from using FSL's packaged template (MNI152NLin2009cAsym) to MNI's, and there were some differences. I thought using FSL's distribution was something we'd copied from HCP. @oesteban will probably know better. There was a problem hiding this comment.
The "MNI" distributed with FSL is an unofficial version created by A. Janke with the same data and methodology of the official Then, the HCP folks resampled the 1mm^3 grid to different resolutions that seem useful to them. We originally placed these files under the During the TemplateFlow changeover, we did not switch from the official, latest MNI template ( Hopefully, this clarifies the spotty connections between TemplateFlow, the "MNI" template(s) and this PR. |
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| select_std = pe.Node(KeySelect(fields=['bold_std']), | ||
| name='select_std', run_without_submitting=True) | ||
| select_std.inputs.key = cifti_volume | ||
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| order_surfs = pe.Node(niu.Function(function=_order_surfs, | ||
| output_names=["surface_files"]), | ||
| name='order_surfs', run_without_submitting=True) | ||
| order_surfs.inputs.targets = list(cifti_spaces) | ||
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| gen_cifti = pe.MapNode(GenerateCifti(), iterfield=["surface_target", "surface_bolds"], | ||
| name="gen_cifti") | ||
| gen_cifti.inputs.TR = metadata.get("RepetitionTime") | ||
| gen_cifti.inputs.surface_target = list(cifti_spaces) | ||
| gen_cifti.inputs.density = fslr_density | ||
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| workflow.connect([ | ||
| (bold_std_trans_wf, select_std, [ | ||
| ('outputnode.templates', 'keys'), | ||
| ('outputnode.bold_std', 'bold_std')]), | ||
| (bold_surf_wf, order_surfs, [('outputnode.surfaces', 'in_surfs')]), | ||
| (order_surfs, gen_cifti, [('surface_files', 'surface_bolds')]), | ||
| (inputnode, gen_cifti, [('subjects_dir', 'subjects_dir')]), | ||
| (select_std, gen_cifti, [ | ||
| ('bold_std', 'bold_file'), | ||
| ('key', 'volume_target')]), | ||
| (gen_cifti, outputnode, [('out_file', 'bold_cifti'), | ||
| ('variant', 'cifti_variant'), | ||
| ('out_metadata', 'cifti_metadata')]), | ||
| ]) | ||
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| # REPORTING ############################################################ | ||
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@@ -1042,6 +1054,15 @@ def _to_join(in_file, join_file): | |
| from niworkflows.interfaces.utils import JoinTSVColumns | ||
| if join_file is None: | ||
| return in_file | ||
| res = JoinTSVColumns(in_file=in_file, join_file=join_file).run() | ||
| return res.outputs.out_file | ||
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| def _order_surfs(targets, in_surfs): | ||
| """Reorder list of surface_files into [L,R] sub-lists""" | ||
| surface_files = [] | ||
| targets = targets if 'fsLR' not in targets else ('fsLR',) | ||
| for target in targets: | ||
| target_files = [f for f in in_surfs if f.endswith("{}.gii".format(target))] | ||
| surface_files.append(target_files) | ||
| return surface_files | ||
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shouldn't this be
?
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Related question: how much time would add to run this with
--output-spaces fsLR <...> --cifti-outputs?There was a problem hiding this comment.
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does
space-fsaverageimply subcortical structures inMNI152NLin2009cAsym?There was a problem hiding this comment.
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not sure exactly how long, the biggest addon would be resampling to fsaverage:164k (resampling to fsLR is fairly quick). Would also spike the size of outputs, as BOLD in fsaverage is fairly big.
If this sounds reasonable, I can add it in