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[Ecat2Nii] Only apply ECAT_CALIBRATION_FACTOR if it has not already b… #268

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merged 6 commits into from
Feb 20, 2024
Merged

[Ecat2Nii] Only apply ECAT_CALIBRATION_FACTOR if it has not already b… #268

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735ded3
[Ecat2Nii] Only apply ECAT_CALIBRATION_FACTOR if it has not already b…
noahg-neuroimage Feb 5, 2024
f1127f5
Update ecat2nii.py
bendhouseart Feb 14, 2024
bdad449
Update pypet2bids/pypet2bids/ecat2nii.py
bendhouseart Feb 16, 2024
0afc5a7
bump version to account for ECAT scaling fix
bendhouseart Feb 16, 2024
1f42813
- minor version
bendhouseart Feb 16, 2024
d02894a
Merge branch 'main' into patch-2
bendhouseart Feb 20, 2024
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8 changes: 6 additions & 2 deletions pypet2bids/pypet2bids/ecat2nii.py
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Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,11 @@ def ecat2nii(ecat_main_header=None,
prompts.append(0)
randoms.append(0)

final_image = img_temp * main_header['ECAT_CALIBRATION_FACTOR']
ecat_cal_units = main_header['CALIBRATION_UNITS'] # Header field designating whether data has already been calibrated
if ecat_cal_units==1: # Calibrate if it hasn't been already
final_image = img_temp * main_header['ECAT_CALIBRATION_FACTOR']
else: # And don't calibrate if CALIBRATION_UNITS is anything else but 1
final_image = img_temp

qoffset_x = -1 * (
((sub_headers[0]['X_DIMENSION'] * sub_headers[0]['X_PIXEL_SIZE'] * 10 / 2) - sub_headers[0][
Expand Down Expand Up @@ -187,7 +191,7 @@ def ecat2nii(ecat_main_header=None,

# TODO img_nii.header['scl_slope'] # this is a NaN array by default but apparently it should be the dose calibration
# factor img_nii.header['scl_inter'] # defaults to NaN array
img_nii.header['scl_slope'] = main_header['ECAT_CALIBRATION_FACTOR']
img_nii.header['scl_slope'] = 0
img_nii.header['scl_inter'] = 0
img_nii.header['slice_end'] = 0
img_nii.header['slice_code'] = 0
Expand Down
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