HCP Pipelines Improvements (ICAFIX, PostFix, RestingStateStats, TaskfMRIAnalysis, londitudinal/cross-sectional logic) #31
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| #!/usr/bin/python | ||
| import json | ||
| import os | ||
| from glob import glob | ||
| import numpy | ||
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| """ | ||
| This script is designed to determine which field maps apply to discrete fMRI scans | ||
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There was a problem hiding this comment. This looks very similar to There was a problem hiding this comment. Hmm. It has been a while since I looked at the get_fieldmap function implemented in pybids so perhaps it has changed, but doesn't the get_fieldmap function just retrieve the fieldmap in which the fmriname is within the "IntendedFor" field? I was under the impression that the "IntendedFor" field does not automatically generate through the BIDS conversion, thus it has to be added manually. What am I missing? There was a problem hiding this comment. Correct. Maybe I misunderstood what your function does. If it's part of a conversion process this repo might not be the best place for it. Maybe it would be better to put it in pybids? There was a problem hiding this comment. I can see why you may have been confused. The comments I provide I very unclear. Obviously I created them when I did not understand what the script was doing myself, and forgot to come through and change them. It is added the "IntendedFor" fields to the fmap json sidecars, so yes I suppose it has more to do with the BIDS conversion. I can propose incorporation to pybids, but perhaps as a catch-all let's leave IntendedFor..py as is for now. |
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| Author - Timothy J Hendrickson | ||
| """ | ||
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| def setup(subject_path): | ||
| if "ses" in os.listdir(subject_path)[0]: | ||
| for item in (os.listdir(subject_path)): | ||
| session_path = subject_path + '/'+ item | ||
| IntendedFor(session_path) | ||
| IntendedFor(subject_path) | ||
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| def IntendedFor(data_path): | ||
| for fmap in sorted(glob(data_path+'/fmap/*.json')): | ||
| with open(fmap, 'r') as f: | ||
| fmap_json = json.load(f) | ||
| f.close() | ||
| if "IntendedFor" in fmap_json: | ||
| del fmap_json["IntendedFor"] | ||
| shim_fmap = fmap_json["ShimSetting"] | ||
| patient_pos_fmap = fmap_json["ImageOrientationPatientDICOM"] | ||
| func_list = [] | ||
| for func in sorted(glob(data_path+'/func/*bold.json')): | ||
| with open(func, 'r') as g: | ||
| func_json = json.load(g) | ||
| shim_func = func_json["ShimSetting"] | ||
| patient_pos_func = func_json["ImageOrientationPatientDICOM"] | ||
| g.close() | ||
| if shim_fmap == shim_func: | ||
| func_nii = glob(data_path+'/func/' +func.split('/')[-1].split('.')[0]+".nii*")[0] | ||
| if "ses" in data_path: | ||
| func_nii = "/".join(func_nii.split("/")[-3:]) | ||
| func_list.append(func_nii) | ||
| else: | ||
| func_nii = "/".join(func_nii.split("/")[-2:]) | ||
| func_list.append(func_nii) | ||
| #elif patient_pos_fmap == patient_pos_func: | ||
| # shim_func_np = numpy.array(shim_func) | ||
| # shim_fmap_np = numpy.array(shim_fmap) | ||
| # diff_shims = shim_fmap_np - shim_func_np | ||
| # print("difference between fieldmap and functional scan is " + str(sum(abs(diff_shims)))) | ||
| # user_input = raw_input("Do you accept this difference? [y/n]: ") | ||
| # if user_input == 'y': | ||
| # func_nii = glob(data_path + '/func/' + func.split('/')[-1].split('.')[0] + ".nii*")[0] | ||
| # if "ses" in data_path: | ||
| # func_nii = "/".join(func_nii.split("/")[-3:]) | ||
| # func_list.append(func_nii) | ||
| # else: | ||
| # func_nii = "/".join(func_nii.split("/")[-2:]) | ||
| # func_list.append(func_nii) | ||
| # else: | ||
| # print(fmap + " does not have match yet...") | ||
| entry = {"IntendedFor": func_list} | ||
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| fmap_json.update(entry) | ||
| with open(fmap, 'w') as f: | ||
| json.dump(fmap_json, f) | ||
| f.close() | ||
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Was there a reason for moving this here?