Hi,
I want to automatically create a volume node from a list of dcm files, without having to “import” the files into Slicer, because the list is already in Slicer as a variable.
Is there a way to do it?
Thanks,
There are lots of special cases with dicom, but if you know the files form a volume this code is what the DICOM module uses under the hood.
Thanks, what is “files” in the code?. I tried to use it but it expects a string.
With:
fileList.InsertNextValue(myList[0])
I’m getting
Traceback (most recent call last):
File "<console>", line 1, in <module>
TypeError: InsertNextValue argument 1: string is required
The elements of my list have all the information about each slide.
For example, myList[0] looks like:
Dataset.file_meta -------------------------------
(0002, 0000) File Meta Information Group Length UL: 254
(0002, 0001) File Meta Information Version OB: b'\x00\x01'
(0002, 0002) Media Storage SOP Class UID UI: CT Image Storage
(0002, 0003) Media Storage SOP Instance UID UI: 1.2.826.0.1.3680043.2.1125.1.52460637011028086951598878742235975
(0002, 0010) Transfer Syntax UID UI: Implicit VR Little Endian
(0002, 0012) Implementation Class UID UI: 1.2.826.0.1.3680043.2.1143.107.104.103.115.3.0.5.111.124.113
(0002, 0013) Implementation Version Name SH: 'GDCM 3.0.5'
(0002, 0016) Source Application Entity Title AE: 'GDCM/ITK 5.1.2'
-------------------------------------------------
(0008, 0008) Image Type CS: ['ORIGINAL', 'PRIMARY', 'AXIAL']
(0008, 0016) SOP Class UID UI: CT Image Storage
(0008, 0018) SOP Instance UID UI: 1.2.826.0.1.3680043.2.1125.1.52460637011028086951598878742235975
(0008, 0020) Study Date DA: '20221024'
(0008, 0021) Series Date DA: '20221024'
(0008, 0023) Content Date DA: '20221024'
(0008, 0030) Study Time TM: '163518'
(0008, 0031) Series Time TM: '163518'
(0008, 0033) Content Time TM: '163518'
(0008, 0050) Accession Number SH: ''
(0008, 0060) Modality CS: 'CT'
(0008, 0070) Manufacturer LO: 'Unknown manufacturer'
(0008, 0090) Referring Physician's Name PN: ''
(0008, 103e) Series Description LO: 'No series description'
(0008, 1090) Manufacturer's Model Name LO: 'Unknown model'
(0010, 0010) Patient's Name PN: 'Anonymous'
(0010, 0020) Patient ID LO: 'IWXMOF'
(0010, 0030) Patient's Birth Date DA: ''
(0010, 0040) Patient's Sex CS: ''
(0018, 0050) Slice Thickness DS: "0.625"
(0018, 5100) Patient Position CS: 'HFS'
(0020, 000d) Study Instance UID UI: 1.2.826.0.1.3680043.2.1125.1.82509780281950280869767406646856996
(0020, 000e) Series Instance UID UI: 1.2.826.0.1.3680043.2.1125.1.52499705098477734239230221067465548
(0020, 0010) Study ID SH: 'SLICER10001'
(0020, 0011) Series Number IS: "1"
(0020, 0013) Instance Number IS: "1"
(0020, 0032) Image Position (Patient) DS: [105.671, 11.5634, -222.079]
(0020, 0037) Image Orientation (Patient) DS: [-1, 0, 0, 0, -1, 0]
(0020, 0052) Frame of Reference UID UI: 1.2.826.0.1.3680043.2.1125.1.45959135399399872453735019046048235
(0020, 1040) Position Reference Indicator LO: ''
(0028, 0002) Samples per Pixel US: 1
(0028, 0004) Photometric Interpretation CS: 'MONOCHROME2'
(0028, 0010) Rows US: 400
(0028, 0011) Columns US: 400
(0028, 0030) Pixel Spacing DS: [.3730469942, .3730469942]
(0028, 0100) Bits Allocated US: 16
(0028, 0101) Bits Stored US: 16
(0028, 0102) High Bit US: 15
(0028, 0103) Pixel Representation US: 1
(0028, 1050) Window Center DS: "100.0"
(0028, 1051) Window Width DS: "800.0"
(0028, 1052) Rescale Intercept DS: "0.0"
(0028, 1053) Rescale Slope DS: "1.0"
(0028, 1054) Rescale Type LO: 'HU'
(7fe0, 0010) Pixel Data OW: Array of 320000 elements
The files argument would be a list of file system paths to binary (“part 10”) dicom datasets.
Are you saying you have a list of pydicom dataset instances instead? As things stand now you would need to write these out to temp files and then load them. Realistically this should be very fast, but if you really need performance you could also look into assembling the volume directly with numpy (but there are many special cases to consider so the result will be highly context dependent, as in knowing in advance what the file contain).
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