SyN-SDC fails for non-default template spaces

[effigies]

See Neurostars #4381.

traits.trait_errors.TraitError: The ‘transforms’ trait of an ApplyTransformsInputSpec instance must be a list of items which are an existing file name or ‘identity’, but a value of [’/scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_facelocalizer_wf/sdc_wf/syn_sdc_wf/ref_2_t1/transform0GenericAffine.mat’, ‘/scratch/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin6Asym/registration/ants_t1_to_mniInverseComposite.h5’, ‘/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/data/fmap_atlas_2_MNI152NLin6Asym_affine.mat’] <class ‘list’> was specified.

Error setting node input:
Node: atlas_2_ref
input: transforms
results_file: /scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_facelocalizer_wf/sdc_wf/syn_sdc_wf/transform_list/result_transform_list.pklz
value: [’/scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_facelocalizer_wf/sdc_wf/syn_sdc_wf/ref_2_t1/transform0GenericAffine.mat’, ‘/scratch/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin6Asym/registration/ants_t1_to_mniInverseComposite.h5’, ‘/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/data/fmap_atlas_2_MNI152NLin6Asym_affine.mat’]

[effigies]

We're missing affine transformations from the fieldmap atlas to other templates.

[oesteban]

This should go into TemplateFlow (it is one of its inception principles and requirements)

[alexlicohen]

Hi all,
I just realized this is still not working; is there a way around this for now?

Node Name: fmriprep_wf.single_subject_NDARAU530GLJ_wf.func_preproc_task_rest_run_2_wf.sdc_wf.syn_sdc_wf.atlas_2_ref
File: /out/fmriprep/sub-NDARAU530GLJ/log/20190707-141844_d5b13a54-1df0-4efa-8851-0b634a2e2e6b/crash-20190708-094223-root-atlas_2_ref-593063a6-e1ca-48d4-80e2-4dde6cfe0d1e.txt
Working Directory: /tmp/work/fmriprep_wf/single_subject_NDARAU530GLJ_wf/func_preproc_task_rest_run_2_wf/sdc_wf/syn_sdc_wf/atlas_2_ref
Inputs:
args:
default_value: 0.0
dimension:
environ: {'NSLOTS': '7'}
float: False
input_image: /usr/local/miniconda/lib/python3.7/site-packages/fmriprep/data/fmap_atlas.nii.gz
input_image_type:
interpolation: Linear
interpolation_parameters:
invert_transform_flags: [True, False, False]
num_threads: 7
out_postfix: _trans
output_image:
print_out_composite_warp_file:
reference_image:
transforms:

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 410, in run
    cached, updated = self.is_cached()
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 296, in is_cached
    hashed_inputs, hashvalue = self._get_hashval()
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 493, in _get_hashval
    self._get_inputs()
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 540, in _get_inputs
    self.set_input(key, deepcopy(output_value))
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 278, in set_input
    setattr(self.inputs, parameter, deepcopy(val))
  File "/usr/local/miniconda/lib/python3.7/site-packages/traits/trait_handlers.py", line 172, in error
    value )
traits.trait_errors.TraitError: The 'transforms' trait of an ApplyTransformsInputSpec instance must be a list of items which are an existing file name or 'identity', but a value of ['/tmp/work/fmriprep_wf/single_subject_NDARAU530GLJ_wf/func_preproc_task_rest_run_2_wf/sdc_wf/syn_sdc_wf/ref_2_t1/transform0GenericAffine.mat', '/tmp/work/fmriprep_wf/single_subject_NDARAU530GLJ_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin6Asym/registration/ants_t1_to_mniInverseComposite.h5', '/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/data/fmap_atlas_2_MNI152NLin6Asym_affine.mat']  was specified.

Error setting node input:
Node: atlas_2_ref
input: transforms
results_file: /tmp/work/fmriprep_wf/single_subject_NDARAU530GLJ_wf/func_preproc_task_rest_run_2_wf/sdc_wf/syn_sdc_wf/transform_list/result_transform_list.pklz
value: ['/tmp/work/fmriprep_wf/single_subject_NDARAU530GLJ_wf/func_preproc_task_rest_run_2_wf/sdc_wf/syn_sdc_wf/ref_2_t1/transform0GenericAffine.mat', '/tmp/work/fmriprep_wf/single_subject_NDARAU530GLJ_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin6Asym/registration/ants_t1_to_mniInverseComposite.h5', '/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/data/fmap_atlas_2_MNI152NLin6Asym_affine.mat']

[rnair07]

Hi - just wondering if there is a solution to this in any of the newer releases? We are doing analysis in subject space and would like to use syn-sdc for distortion correction. Thanks.

[JeroenBlommaert]

Hi - just wondering if there is a solution to this in any of the newer releases? We are doing analysis in subject space and would like to use syn-sdc for distortion correction. Thanks.

The work-around works perfectly, just specify explicitly the necessary atlas space

[rnair07]

Hi - just wondering if there is a solution to this in any of the newer releases? We are doing analysis in subject space and would like to use syn-sdc for distortion correction. Thanks.

The work-around works perfectly, just specify explicitly the necessary atlas space

@JeroenBlommaert : could you elaborate on this please. What is the work around?

[JeroenBlommaert]

Hi - just wondering if there is a solution to this in any of the newer releases? We are doing analysis in subject space and would like to use syn-sdc for distortion correction. Thanks.

The work-around works perfectly, just specify explicitly the necessary atlas space

@JeroenBlommaert : could you elaborate on this please. What is the work around?

I was referring to this thread mentioned above.
Basically, you have to add MNI152NLin2009cAsym to your output spaces