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319 standardize radiochemistry metadata case order #321

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Sep 12, 2024
Merged

319 standardize radiochemistry metadata case order #321

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ba2557a
Bump Pandas Version (#317)
bendhouseart Aug 12, 2024
f312bbd
added reordering for Isotope Number
bendhouseart Aug 16, 2024
0135f6d
Merge branch '263-telementry-add-tracking-of-code-usage' into 319-sta…
bendhouseart Sep 12, 2024
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2 changes: 1 addition & 1 deletion ecat_validation/Readme.md
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Expand Up @@ -116,4 +116,4 @@ pip install pypet2bids
ecatpet2bids ECAT7_multiframe.v.gz --convert
```

This illustrates [what metadata are extracted from the ecat file](https://github.com/openneuropet/PET2BIDS/blob/main/ecat_validation/ECAT7_multiframe.json) - which does not comform with BIDS because radiochemistry and pharmaceutical metadata are missing.
This illustrates [what metadata are extracted from the ecat file](https://github.com/openneuropet/PET2BIDS/blob/main/ecat_validation/ECAT7_multiframe.json) - which does not conform with BIDS because radiochemistry and pharmaceutical metadata are missing.
4 changes: 2 additions & 2 deletions matlab/dcm2niix4pet.m
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Expand Up @@ -28,7 +28,7 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
% - *p* = 'y'; % Philips precise float (not display) scaling (y/n, default y)
% - *v* = 1; % verbose (n/y or 0/1/2, default 0) [no, yes, logorrheic]
% - *w* = 2; % write behavior for name conflicts (0,1,2, default 2: 0=skip duplicates, 1=overwrite, 2=add suffix)
% - *x* = 'n'; % crop 3D acquisitions (y/n/i, default n, use 'i'gnore to neither crop nor rotate 3D acquistions)
% - *x* = 'n'; % crop 3D acquisitions (y/n/i, default n, use 'i'gnore to neither crop nor rotate 3D acquisitions)
% - *z* = 'n'; % gz compress images (y/o/i/n/3, default y) [y=pigz, o=optimal pigz, i=internal:miniz, n=no, 3=no,3D]
% :param notrack: boolean to Opt-out of sending tracking information of this run to the PET2BIDS developers. This information helps to improve PET2BIDS and provides an indicator of real world usage crucial for obtaining funding."
%
Expand Down Expand Up @@ -102,7 +102,7 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
p = 'y'; % Philips precise float (not display) scaling (y/n, default y)
v = 1; % verbose (n/y or 0/1/2, default 0) [no, yes, logorrheic]
w = 2; % write behavior for name conflicts (0,1,2, default 2: 0=skip duplicates, 1=overwrite, 2=add suffix)
x = 'n'; % crop 3D acquisitions (y/n/i, default n, use 'i'gnore to neither crop nor rotate 3D acquistions)
x = 'n'; % crop 3D acquisitions (y/n/i, default n, use 'i'gnore to neither crop nor rotate 3D acquisitions)
z = 'y'; % gz compress images (y/o/i/n/3, default y) [y=pigz, o=optimal pigz, i=internal:miniz, n=no, 3=no,3D]

%% check dcm2nii inputs
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76 changes: 38 additions & 38 deletions metadata/PET_Radionuclide.mkd
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Expand Up @@ -2,41 +2,41 @@

Table taken from https://dicom.nema.org/medical/Dicom/2016b/output/chtml/part16/sect_CID_4020.html

| Code Value | Code Meaning |
|:----------:|:---------------:|
| C-105A1 | ^11^Carbon |
| C-107A1 | ^13^Nitrogen |
| C-1018C | ^14^Oxygen |
| C-B1038 | ^15^Oxygen |
| C-111A1 | ^18^Fluorine |
| C-155A1 | ^22^Sodium |
| C-135A4 | ^38^Potassium |
| 126605 | ^43^Scandium |
| 126600 | ^44^Scandium |
| C-166A2 | ^45^Titanium |
| 126601 | ^51^Manganese |
| C-130A1 | ^52^Iron |
| C-149A1 | ^52^Manganese |
| 126607 | ^52m^Manganese |
| C-127A4 | ^60^Copper |
| C-127A1 | ^61^Copper |
| C-127A5 | ^62^Copper |
| C-141A1 | ^62^Zinc |
| C-127A | ^64^Copper |
| C-131A1 | ^66^Gallium |
| C-131A3 | ^68^Gallium |
| C-128A2 | ^68^Germanium |
| 126602 | ^70^Arsenic |
| C-115A2 | ^72^Arsenic |
| C-116A2 | ^73^Selenium |
| C-113A1 | ^75^Bromine |
| C-113A2 | ^76^Bromine |
| C-113A3 | ^77^Bromine |
| C-159A2 | ^82^Rubidium |
| C-162A3 | ^86^Yttrium |
| C-168A4 | ^89^Zirconium |
| 126603 | ^90^Niobium |
| C-162A7 | ^90^Yttrium |
| C-163AA | ^94m^Technetium |
| C-114A5 | ^124^Iodine |
| 126606 | ^152^Terbium |
| Code Value | Code Meaning | Isotope Abbreviation |
|:----------:|:---------------:|:--------------------:|
| C-105A1 | ^11^Carbon | 11C |
| C-107A1 | ^13^Nitrogen | 13N |
| C-1018C | ^14^Oxygen | 14O |
| C-B1038 | ^15^Oxygen | 150 |
| C-111A1 | ^18^Fluorine | 18F |
| C-155A1 | ^22^Sodium | 22Na |
| C-135A4 | ^38^Potassium | 38K |
| 126605 | ^43^Scandium | 43Sc |
| 126600 | ^44^Scandium | 44Sc |
| C-166A2 | ^45^Titanium | 45Ti |
| 126601 | ^51^Manganese | 51Mn |
| C-130A1 | ^52^Iron | 52Fe |
| C-149A1 | ^52^Manganese | 52Mn |
| 126607 | ^52m^Manganese | 52mMn |
| C-127A4 | ^60^Copper | 60Cu |
| C-127A1 | ^61^Copper | 61Cu |
| C-127A5 | ^62^Copper | 62Cu |
| C-141A1 | ^62^Zinc | 62Zn |
| C-127A | ^64^Copper | 64Cu |
| C-131A1 | ^66^Gallium | 66Ga |
| C-131A3 | ^68^Gallium | 68Ga |
| C-128A2 | ^68^Germanium | 68Ge |
| 126602 | ^70^Arsenic | 70As |
| C-115A2 | ^72^Arsenic | 72As |
| C-116A2 | ^73^Selenium | 73Se |
| C-113A1 | ^75^Bromine | 75Br |
| C-113A2 | ^76^Bromine | 76Br |
| C-113A3 | ^77^Bromine | 77Br |
| C-159A2 | ^82^Rubidium | 82Rb |
| C-162A3 | ^86^Yttrium | 86Y |
| C-168A4 | ^89^Zirconium | 89Zr |
| 126603 | ^90^Niobium | 90Nb |
| C-162A7 | ^90^Yttrium | 90Y |
| C-163AA | ^94m^Technetium | 94mTc |
| C-114A5 | ^124^Iodine | 124I |
| 126606 | ^152^Terbium | 152Tb |
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