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A buch of changes (hot fixes) to ensure nipype 1.0 compatibility #305

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A buch of changes (hot fixes) to ensure nipype 1.0 compatibility #305

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2 changes: 1 addition & 1 deletion pypreprocess/configure_spm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -485,7 +485,7 @@ def _configure_spm_using_mcr(spm_mcr, spm_dir, spm_version):
_logger.info('setting SPM MCR path to "{}" '
'and "use_mcr" to True'.format(spm_mcr))
spm.SPMCommand.set_mlab_paths(
matlab_cmd='{} run script'.format(spm_mcr), use_mcr=True)
matlab_cmd='{} batch'.format(spm_mcr), use_mcr=True)
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@KamalakerDadi KamalakerDadi Apr 11, 2018

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Good catch on this. They have deprecated using "run" from recent standalone versions for SPM12. More details on this can be found here https://github.com/spm/spm12/blob/master/spm_standalone.m

I am wandering whether this might again get into script running errors when users fall back to slightly older standalone versions ?

_logger.info('SPM configuration succeeded using SPM MCR.')


Expand Down
22 changes: 7 additions & 15 deletions pypreprocess/nipype_preproc_spm_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -196,7 +196,6 @@ def _do_subject_slice_timing(subject_data, TR, TA=None, spm_dir=None,
time_acquisition=TA, num_slices=nslices,
ref_slice=ref_slice + 1,
slice_order=list(slice_order + 1), # SPM
ignore_exception=True
)
if stc_result.outputs is None:
subject_data.failed = True
Expand Down Expand Up @@ -495,7 +494,6 @@ def _do_subject_coregister(subject_data, reslice=False, spm_dir=None,
source=coreg_source,
apply_to_files=apply_to_files,
jobtype=jobtype,
ignore_exception=True
)

# failed node ?
Expand Down Expand Up @@ -633,7 +631,6 @@ def _do_subject_segment(subject_data, output_modulated_tpms=True, spm_dir=None,
wm_output_type=gm_output_type,
csf_output_type=csf_output_type,
tissue_prob_maps=[GM_TEMPLATE, WM_TEMPLATE, CSF_TEMPLATE],
ignore_exception=True
)

# failed node
Expand Down Expand Up @@ -746,7 +743,7 @@ def _do_subject_normalize(subject_data, fwhm=0., anat_fwhm=0., caching=True,
output_dir=subject_data.scratch)
normalize_result = normalize(
source=subject_data.anat, template=t1_template,
write_preserve=False, ignore_exception=True)
write_preserve=False)
parameter_file = normalize_result.outputs.normalization_parameters
else:
parameter_file = subject_data.nipype_results[
Expand Down Expand Up @@ -777,7 +774,7 @@ def _do_subject_normalize(subject_data, fwhm=0., anat_fwhm=0., caching=True,
apply_to_files=apply_to_files,
write_voxel_sizes=list(write_voxel_sizes),
# write_bounding_box=[[-78, -112, -50], [78, 76, 85]],
write_interp=1, jobtype='write', ignore_exception=True)
write_interp=1, jobtype='write')

# failed node ?
if normalize_result.outputs is None:
Expand Down Expand Up @@ -807,9 +804,7 @@ def _do_subject_normalize(subject_data, fwhm=0., anat_fwhm=0., caching=True,
write_voxel_sizes=list(write_voxel_sizes),
write_wrap=[0, 0, 0],
write_interp=1,
jobtype='write',
ignore_exception=True
)
jobtype='write')

# failed node
subject_data.nipype_results['normalize_%s' % brain_name
Expand Down Expand Up @@ -933,7 +928,7 @@ def _do_subject_smooth(subject_data, fwhm, anat_fwhm=None, spm_dir=None,
in_files = [getattr(subject_data, x) for x in anat_like]

smooth_result = smooth(
in_files=in_files, fwhm=width, ignore_exception=True)
in_files=in_files, fwhm=width)

# failed node ?
subject_data.nipype_results['smooth'][brain_name] = smooth_result
Expand Down Expand Up @@ -1025,7 +1020,7 @@ def _do_subject_dartelnorm2mni(subject_data,
flowfield_files=subject_data.dartel_flow_fields,
template_file=template_file,
modulate=output_modulated_tpms, # don't modulate
fwhm=anat_fwhm, ignore_exception=True, **tricky_kwargs)
fwhm=anat_fwhm, **tricky_kwargs)
setattr(subject_data, "mw" + tissue,
dartelnorm2mni_result.outputs.normalized_files)

Expand All @@ -1034,7 +1029,6 @@ def _do_subject_dartelnorm2mni(subject_data,
apply_to_files=subject_data.anat,
flowfield_files=subject_data.dartel_flow_fields,
template_file=template_file,
ignore_exception=True,
modulate=output_modulated_tpms,
fwhm=anat_fwhm,
**tricky_kwargs
Expand All @@ -1049,7 +1043,6 @@ def _do_subject_dartelnorm2mni(subject_data,
createwarped_result = createwarped(
image_files=subject_data.func,
flowfield_files=subject_data.dartel_flow_fields,
ignore_exception=True
)
subject_data.func = createwarped_result.outputs.warped_files

Expand Down Expand Up @@ -1406,9 +1399,8 @@ def _do_subjects_newsegment(

# run node
newsegment_result = newsegment(
channel_files=[subject_data.anat for subject_data in subjects],
tissues=TISSUES,
ignore_exception=True)
channel_files=[subject_data.anat.replace(".nii.gz", ".nii")
for subject_data in subjects], tissues=TISSUES)
if newsegment_result.outputs is None:
return
else:
Expand Down