How do I make sure two imported .nrrd files are plotted in the same coordinate frame when using nrrdread?

Hi all,

I have an MRI volume and a segmentation from a scene in 3D Slicer, and I need to do some analysis in MATLAB. In Slicer, the two entities overlay each other properly, but when I import them into MATLAB things don't align anymore. In Slicer, all transforms have been hardened.

There are a lot of properties in the .nrrd headers (shown below my code), and I'm not sure if I need to handle any of them explicitly or if MATLAB knows what to do with it automatically when I use 'nrrdread'.

My code is as follows:

vol_A = double(nrrdread('path/to/nrrd_file_A'));
vol_B = double(nrrdread('path/to/nrrd_file_B'));


%% Transform stuff needs to go here so vol_A and vol_B are aligned %%
% I imagine I need to use imrotate3 and imtranslate, but can't figure out
% what values to use

% Find the non-zero indices in volume B and mark them in volume A with a value of 1024
% so we can see them easily
[x,y,z] = ind2sub(size(vol_B), find(vol_B));
for i = 1:size(x, 1)
    vol_A(x,y,z) = 1024;
end

% Create alphamap and colormap to make the 1024 values stick out in bright
% red
alpha = [0, 0, 0.02, 0.037, 0.01, 0.02, 1];
color = [0 0 0; 43 0 0; 103 37 20; 199 155 97; 216 213 201; 255 255 255; 255 0 0]/255;
intensity = [0, 40, 80, 120, 800, 1000, 1024];
queryPoints = linspace(min(intensity), max(intensity), 256);
alphamap = interp1(intensity, alpha, queryPoints);
colormap = interp1(intensity, color, queryPoints);

% Display the combined volume
volshow(vol_A, Colormap=colormap, Alphamap=alphamap);

Header file for .nrrd file A

NRRD0004
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format.html
type: unsigned char
dimension: 3
space: left-posterior-superior
sizes: 224 224 250
space directions: (0,0.96363633871077981,0) (0,0,-0.96363633871077981) (-0.95999905383251116,0,0)
kinds: domain domain domain
encoding: gzip
space origin: (102.84023291351068,-109.67142070125807,102.80120362861894)
Segment0_Color:=0.501961 0.682353 0.501961
Segment0_ColorAutoGenerated:=1
Segment0_Extent:=1 93 107 167 77 161
Segment0_ID:=Segment_1
Segment0_LabelValue:=1
Segment0_Layer:=0
Segment0_Name:=Lesion
Segment0_NameAutoGenerated:=0
Segment0_Tags:=Segmentation.Status:inprogress|TerminologyEntry:Segmentation category and type - 3D Slicer General Anatomy list~SRT^T-D0050^Tissue~SRT^T-D0050^Tissue~^^~Anatomic codes - DICOM master list~^^~^^|
Segmentation_ContainedRepresentationNames:=Binary labelmap|
Segmentation_ConversionParameters:=Collapse labelmaps|1|Merge the labelmaps into as few shared labelmaps as possible 1 = created labelmaps will be shared if possible without overwriting each other.&Compute surface normals|1|Compute surface normals. 1 (default) = surface normals are computed. 0 = surface normals are not computed (slightly faster but produces less smooth surface display).&Crop to reference image geometry|0|Crop the model to the extent of reference geometry. 0 (default) = created labelmap will contain the entire model. 1 = created labelmap extent will be within reference image extent.&Decimation factor|0.0|Desired reduction in the total number of polygons. Range: 0.0 (no decimation) to 1.0 (as much simplification as possible). Value of 0.8 typically reduces data set size by 80% without losing too much details.&Fractional labelmap oversampling factor|1|Determines the oversampling of the reference image geometry. All segments are oversampled with the same value (value of 1 means no oversampling).&Joint smoothing|0|Perform joint smoothing.&Oversampling factor|1|Determines the oversampling of the reference image geometry. If it's a number, then all segments are oversampled with the same value (value of 1 means no oversampling). If it has the value "A", then automatic oversampling is calculated.&Reference image geometry|0;0;0.959999053832511;-102.84023291351069;-0.96363633871078;0;0;109.67142070125809;0;-0.96363633871078;0;102.80120362861896;0;0;0;1;0;223;0;223;0;249;|Image geometry description string determining the geometry of the labelmap that is created in course of conversion. Can be copied from a volume, using the button.&Smoothing factor|0|Smoothing factor. Range: 0.0 (no smoothing) to 1.0 (strong smoothing).&Threshold fraction|0.5|Determines the threshold that the closed surface is created at as a fractional value between 0 and 1.&
Segmentation_MasterRepresentation:=Binary labelmap
Segmentation_ReferenceImageExtentOffset:=0 0 0

Header file for .nrrd file B

NRRD0004
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format.html
type: double
dimension: 3
space: left-posterior-superior
sizes: 256 256 250
space directions: (-0.039238430422844015,-0.87955116855925952,-0.022804295261199786) (-0.066398172718697565,0.025722025661534198,-0.8778380308883027) (0.95606014202768841,-0.040745765711721449,-0.073508674494034767)
kinds: domain domain domain
endian: little
encoding: gzip
space origin: (-105.56082078190065,113.93606355056932,123.98372655856895)

[Avni]

Hi, can you share nrrd files?