I have encountered another problem with importing “.seq.nrrd” sequence files. I have recorded a sequence file with the PLUS remote module via Slicer containing US and tracker data. When I try to import this directly into Slicer, it reads the volume voxel data but not the spacing / offset / tracking …

Plus saves the raw data (original transforms and uncalibrated image data) to sequence files, so you need to apply calibration as explained in SlicerIGT tutorials.

That is exactly what I was trying to do (import the PLUS raw data into Slicer to run the calibration). But for this it is necessary to read the volumes AND the original transforms from the .seq.nrrd file. I am not sure what I am doing wrong since only the volumes appear in the data module but not th…

Do you have transforms in the .seq.nrrd file? Have you installed Sequences extension? Can you replay the sequence using sequence browser toolbar (play/pause/prev/next buttons)?

Yes to all of your questions. The .seq.nrrd file saved by PLUS contains a header like the example included below. In this case I have used the “FakeTracker” for simulation and as you can see the transforms are included in the PLUS file. When replaying this file via PLUS remote, the volumes and the t…

Can you upload the sequence file and application log (menu: Help/Report a bug) to Dropbox/OneDrive/Gdrive and post the link here?

Sure, here are the sequence file, the config file I used for recording in PLUS and the Slicer log: https://www.dropbox.com/s/8ld1r30l0affqxc/4DUS-Sequence.zip?dl=0 Thanks!

Thanks for the data. It seems that Sequences can only import tracked image data from seq.mha or seq.mhd files (and not from seq.nrrd or seq.nhdr). If you save the data in Plus as seq.mha then you can load it as “Sequence Metafile” instead of “Volume Sequence”. I’m not sure if Plus can save 4D track…

I have tried to save the data in a .seq.mhd file via PLUS but when I try to import the file into Slicer as a Sequence Metafile it just crashes. Maybe you could have another look at the files? https://www.dropbox.com/s/32he9eb4w0rcm4r/4DUS-Sequence-MHD.zip?dl=0 Do you reckon this is a problem with …

Slicer should not crash when trying to import the sequence, so it is an issue in Sequences extension. Could you please submit a bug report for Sequences extension .

I submitted an issue for the Sequences extension ( https://github.com/SlicerRt/Sequences/issues/52 ). Looking forward to your reply!

Importing of position-tracked ultrasound sequence

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Importing of position-tracked ultrasound sequence

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