Visualize tracked ultrasound in 3D with PNG images and pose matrices

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1

Hi, I’m trying to create a sequence file from a folder of ultrasound images in png format with poses stored in a csv file and then visualize in 3D.
I successfully created the .mhd header file containing the pose information and the poses can be visualized in Slicer. The file “Scan1.seq.mhd” looks like below:

ObjectType = Image
NDims = 3
AnatomicalOrientation = RAI
BinaryData = True
BinaryDataByteOrderMSB = False
CenterOfRotation = 0 0 0
CompressedData = False
ElementSpacing = 1 1 1
Offset = 0 0 0
TransformMatrix = 1 0 0 0 1 0 0 0 1
UltrasoundImageOrientation = MFA
UltrasoundImageType = BRIGHTNESS
Seq_Frame0000_ImageToReferenceTransform = 0.25880223 -0.96586309 0.01139754 99.35319738 -0.00294990 0.01100917 0.99993505 19.23409344 -0.96592583 -0.25881905 0.00000000 4.28620653 0.00000000 0.00000000 0.00000000 1.00000000
Seq_Frame0000_ImageToReferenceTransformStatus = OK
Seq_Frame0000_Timestamp = 0.000
Seq_Frame0000_ImageStatus = OK
Seq_Frame0001_ImageToReferenceTransform = 0.25868718 -0.96543371 0.03191713 99.30936271 -0.00826076 0.03082958 0.99949052 18.11578949 -0.96592583 -0.25881905 0.00000000 4.28620653 0.00000000 0.00000000 0.00000000 1.00000000
Seq_Frame0001_ImageToReferenceTransformStatus = OK
Seq_Frame0001_Timestamp = 0.300
Seq_Frame0001_ImageStatus = OK
Seq_Frame0002_ImageToReferenceTransform = 0.25844698 -0.96453726 0.05360077 99.21784580 -0.01387290 0.05177437 0.99856245 16.90844963 -0.96592583 -0.25881905 -0.00000000 4.28620653 0.00000000 0.00000000 0.00000000 1.00000000
Seq_Frame0002_ImageToReferenceTransformStatus = OK
Seq_Frame0002_Timestamp = 0.600
Seq_Frame0002_ImageStatus = OK
Seq_Frame0003_ImageToReferenceTransform = 0.25810672 -0.96326738 0.07414098 99.08820620 -0.01918910 0.07161468 0.99724777 15.78648773 -0.96592583 -0.25881905 -0.00000000 4.28620653 0.00000000 0.00000000 0.00000000 1.00000000
Seq_Frame0003_ImageToReferenceTransformStatus = OK
Seq_Frame0003_Timestamp = 0.900
Seq_Frame0003_ImageStatus = OK
…
ElementDataFile = Scan1.seq.nrrd

However, when I load this file into slicer as Sequence Metafile, it cannot pull the image data into the Slicer even though the Scan1.seq.nrrd file is under same directory as the .mhd metafile. I created the “Scan1.seq.nrrd” by opening the folder containing png images in slicer as volume, and save it as .nrrd file. I wonder if I should convert the png images into raw data file in a different way?

Also I wonder if I should set the ultrasound image spacing parameter in .mhd file? E.g., if my pixel spacing is 0.27mm, should I change the ElementSpacing = 0.27 0.27 0.27?

I appreciate any help!

2

Update: I’m still struggling on creating the sequence file correctly, but here is what I have tried so far

Attempt 1: Using the MultiVolume Importer
I tried to use the MultiVolume Importer to open the folder containing my png ultrasound images, and save the MultiVolume node as an nrrd file. Then I load the file in Slicer as Sequence, the result looks good (as shown below).

image
image849×462 63 KB

However, if I tried to load the nrrd file (contains all my images) with my custom mhd file, it will not show the data at all. I’m attaching both files in the links.
image

If I open up the nrrd file in text editor, I see it actually contains a header saying the dimension is 4, which violates the Sequence file rule of NDims=3.
image

Attempt 2: Creating binary file using numpy array
So I tried to read every image into python and generate the numpy array (dtype=uint8) with size 660 x 616 x 417 (width x height x frames), then save the array into binary file and try to load it with the mhd file again. This time it shows noisy data which looks confusing.

image
image975×530 71.2 KB

Can I get any advice on creating a custom sequence file from stored images? Thank you in advance!