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Port resolutions changes from gitlab to github.
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@kathy-snider
kathy-snider committed Jan 29, 2020
1 parent 49692db commit 05a3a72
Showing 1 changed file with 64 additions and 17 deletions.
81 changes: 64 additions & 17 deletions dcan_bold_proc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,11 @@ def _cli():
'brain_radius': args.brain_radius,
'setup': args.setup,
'teardown': args.teardown,
'tasklist': args.tasklist
'tasklist': args.tasklist,
'fmri_res': args.fmri_res,
'roi_res': args.roi_res,
'no_aparc': args.no_aparc,
'sigma': args.sigma if args.sigma else args.roi_res
}

return interface(**kwargs)
Expand Down Expand Up @@ -108,6 +112,28 @@ def generate_parser(parser=None):
help='output folder which contains all files produced by the dcan '
'fmri-pipeline. Used for setting up standard inputs and outputs'
)
setup = parser.add_argument_group(
'wm/vent regressors', 'options for obtaining white matter and '
'ventricle signal regressors')
setup.add_argument(
'--fmri-res', type=float, default=2.,
help='isotropic resolution (mm) for final fmri volume. Default is 2.'
)
setup.add_argument(
'--roi-res', type=float, default=2.,
help='isotropic resolution (mm) for vent/wm roi volumes. Default is '
'2.'
)
setup.add_argument(
'--sigma', type=float,
help='sigma for gaussian kernel used to erode rois prior to signal '
'extraction. Default is to use roi resolution'
)
setup.add_argument(
'--no-aparc', action='store_true',
help='flag to use original freesurfer LR white matter labels instead '
'of parcellated labels.'
)
bold_filter = parser.add_argument_group(
'bold signal filtering', 'bold signal filtering parameters.')
bold_filter.add_argument(
Expand Down Expand Up @@ -189,6 +215,7 @@ def generate_parser(parser=None):
'determine motion filter parameters. Columns, start time, and '
'frequency will also need to be specified. NOT IMPLEMENTED.'
)


return parser

Expand All @@ -199,7 +226,8 @@ def interface(subject, output_folder, task=None, fd_threshold=None,
motion_filter_order=None, band_stop_min=None,
band_stop_max=None, skip_seconds=None, brain_radius=None,
contiguous_frames=None, setup=False, teardown=None,
tasklist=None, **kwargs):
tasklist=None, fmri_res=2., roi_res=2., no_aparc=False,
**kwargs):
"""
main function with 3 modes:
setup, task, and teardown.
Expand Down Expand Up @@ -252,7 +280,7 @@ def interface(subject, output_folder, task=None, fd_threshold=None,
'Movement_Regressors.txt'),
'output_dtseries_basename': '%s_%s_Atlas' % (task, version_name),
'segmentation': os.path.join(output_folder, 'MNINonLinear', 'ROIs',
'wmparc.2.nii.gz')
'wmparc.%g.nii.gz' % roi_res)
}
input_spec.update(kwargs.get('input_spec', {}))
output_spec = {
Expand All @@ -268,17 +296,20 @@ def interface(subject, output_folder, task=None, fd_threshold=None,
'analyses_v2','timecourses'),
'result_dir': os.path.join(output_folder, 'MNINonLinear', 'Results',
task, version_name),
'summary_folder': os.path.join(output_folder, 'summary_%s' % version_name),
'summary_folder': os.path.join(output_folder,
'summary_%s' % version_name),
'vent_mask': os.path.join(output_folder, 'MNINonLinear',
'vent_2mm_%s_mask_eroded.nii.gz' % subject),
'vent_%gmm_%s_mask_eroded.nii.gz' % \
(fmri_res, subject)),
'vent_mean_signal': os.path.join(output_folder, 'MNINonLinear',
'Results', task, version_name,
'%s_vent_mean.txt' % task),
'wm_mask': os.path.join(output_folder, 'MNINonLinear',
'wm_2mm_%s_mask_eroded.nii.gz' % subject),
'wm_mean_signal': os.path.join(output_folder, 'MNINonLinear', 'Results',
task, version_name, '%s_wm_mean.txt' %
task)
'wm_%gmm_%s_mask_eroded.nii.gz' % \
(fmri_res, subject)),
'wm_mean_signal': os.path.join(output_folder, 'MNINonLinear',
'Results', task, version_name,
'%s_wm_mean.txt' % task)
}
output_spec.update(kwargs.get('output_spec', {}))

Expand All @@ -305,9 +336,16 @@ def interface(subject, output_folder, task=None, fd_threshold=None,
if not os.path.exists(output_spec['summary_folder']):
os.mkdir(output_spec['summary_folder'])

if no_aparc:
label_override = dict(wm_lt_R=2, wm_ut_R=2, wm_lt_L=41,
wm_ut_L=41)
else:
label_override = {}

# create white matter and ventricle masks for regression
make_masks(input_spec['segmentation'], output_spec['wm_mask'],
output_spec['vent_mask'])
output_spec['vent_mask'], fmri_res=fmri_res,
roi_res=roi_res, **label_override)

elif teardown:
output_results = os.path.join(output_folder, 'MNINonLinear', 'Results')
Expand Down Expand Up @@ -419,9 +457,9 @@ def interface(subject, output_folder, task=None, fd_threshold=None,

# get ventricular and white matter signals
mean_roi_signal(input_spec['fmri_volume'], output_spec['wm_mask'],
output_spec['wm_mean_signal'])
output_spec['wm_mean_signal'], fmri_res, roi_res)
mean_roi_signal(input_spec['fmri_volume'], output_spec['vent_mask'],
output_spec['vent_mean_signal'])
output_spec['vent_mean_signal'], fmri_res, roi_res)

# run signal processing on dtseries
matlab_input = {
Expand Down Expand Up @@ -476,7 +514,7 @@ def get_repetition_time(fmri):
return repetition_time


def mean_roi_signal(fmri, mask, output):
def mean_roi_signal(fmri, mask, output, fmri_res=2., roi_res=2.):
"""
:param fmri: path to fmri nifti
:param mask: path to mask/roi nifti
Expand All @@ -485,6 +523,12 @@ def mean_roi_signal(fmri, mask, output):
:return: None
"""
cmd = 'fslmeants -i {fmri} -o {output} -m {mask}'
if fmri_res != roi_res:
resamplecmd = 'flirt -interp nearestneighbour -in {mask} -ref ' \
'{fmri} -applyxfm -out {mask}'
resamplecmd = resamplecmd.format(fmri=fmri, output=output, mask=mask,
fmri_res=fmri_res)
subprocess.call(resamplecmd.split())
cmd = cmd.format(fmri=fmri, output=output, mask=mask)
subprocess.call(cmd.split())

Expand All @@ -507,7 +551,8 @@ def make_masks(segmentation, wm_mask_out, vent_mask_out, **kwargs):
wd = os.path.dirname(wm_mask_out)
# set parameter defaults
defaults = dict(wm_lt_R=2950, wm_ut_R=3050, wm_lt_L=3950, wm_ut_L=4050,
vent_lt_R=43, vent_ut_R=43, vent_lt_L=4, vent_ut_L=4)
vent_lt_R=43, vent_ut_R=43, vent_lt_L=4, vent_ut_L=4,
roi_res=2)
# set temporary filenames
tempfiles = {
'wm_mask_L': os.path.join(wd, 'tmp_left_wm.nii.gz'),
Expand All @@ -528,19 +573,21 @@ def make_masks(segmentation, wm_mask_out, vent_mask_out, **kwargs):
'fslmaths {segmentation} -thr {wm_lt_R} -uthr {wm_ut_R} {wm_mask_R}',
'fslmaths {segmentation} -thr {wm_lt_L} -uthr {wm_ut_L} {wm_mask_L}',
'fslmaths {wm_mask_R} -add {wm_mask_L} -bin {wm_mask}',
'fslmaths {wm_mask} -kernel gauss 2 -ero {wm_mask_out}',
'fslmaths {wm_mask} -kernel gauss {roi_res:g} -ero {wm_mask_out}',
'fslmaths {segmentation} -thr {vent_lt_R} -uthr {vent_ut_R} '
'{vent_mask_R}',
'fslmaths {segmentation} -thr {vent_lt_L} -uthr {vent_ut_L} '
'{vent_mask_L}',
'fslmaths {vent_mask_R} -add {vent_mask_L} -bin {vent_mask}',
'fslmaths {vent_mask} -kernel gauss 2 -ero {vent_mask_out}'
'fslmaths {vent_mask} -kernel gauss {roi_res:g} -ero {vent_mask_out}'
]
# format and run commands

# get params
defaults.update(kwargs)
kwargs.update(defaults)
kwargs.update(iofiles)
kwargs.update(tempfiles)
# format and run commands
for cmdfmt in cmdlist:
cmd = cmdfmt.format(**kwargs)
subprocess.call(cmd.split())
Expand Down

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