Single slice nifti loaded as 2 slice volume

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1

Dear all, I’m having a issue while loading a single slice nifti file.

When I load this file (1.nii) into slicer, the volume module informs me about that it is a 2 slice volume but it should be 1 slice only.

I created the file using matlab, when I load it into imageJ or matlab, both show 1 slice volume.

Using the same library from Matlab I created a nifti file containing a mask (mascaraAlineacion.nii), which is correctly loaded as 1 slice labelmap.

I’m quite sure that both files only differ in the content of the image and glmin/glmax values contained into the header.

Is this a bug? or should I take care of any special requirement for the nii header?

Thank you in advance.

2

I don’t have an answer to your specific question, but why don’t you look at the MatlabBridge extension instead of writing NIfTI file?

3

As a quick test, you can use nrrdwrite.m function of MatlabBridge to write a nrrd image file - https://github.com/PerkLab/SlicerMatlabBridge/tree/master/MatlabCommander/commandserver

The mascaraAlineacion.nii file that you’ve sent the link to, can be loaded without any warnings in the nightly build. It seems to be a binary image, so you may want to load it as a labelmap volume (in “Add data” dialog, click “Show options”, then click “Labelmap”).

4

I loaded this file in to three different Slicer versions I had running (2018/07-25 & 06-13, and 4.8.1). All of them show dimensions as 512x512x1 mm in the Volumes module.

5

Dear all, thank you very muh for your replies.

I have tested this on versions 4.5.0-1 and 4.9.0 (18/07/2018). On both versions the problem appears when I do NOT select the “single file” option when I load the volumes.

I intend to use Slicer from Matlab using a system call to send a CLI command. I intend to perform several rigid registrations. May I check if Brainsfit is using the correct volumes?

Thank you in advance.

6

If you have multiple slices with similar enough names in the same folder then Slicer can load them as a 3D volume. If you prefer to load just a single slice then check single file option, put files in separate folders, or use different file names.

I’m not sure if BRAINS other registration modules support single-slice volume registration, you may need to resample the single-slice volume to have at least 3 slices (for example, using Crop and resample module, as described in other topics in this forum). If you have any problems with registration, please post it in a new topic and give high-level overview, what you would like to do, and any specific problem that you have.

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