I am currently using MrView-Mrtrix to analyze MRI-DTI data from a very small animal model.
I am having problems in doing the manual segmentation of the ROIs because in MrView it’s not possible to re-orient the MRI scan into a projection of the brain which is symmetrical for doing the actual segmentation.
I can re-orient the MRI view into a symmetrical projection but then when I click on the image to trace the ROIs and do the segmentation, the view goes back to the asymmetrical view of the brain in which the sample was scanned.
As it’s very hard for our brain samples to be placed in the proper orientation for scanning, I need a software that allows me to do the manual segmentation on a re-oriented projection different from the one obtained during the MRI-DTI scan.
Is it possible to do this with your software?
Would the 3D slicer allow it?
Thanks a lot
In Slicer’s Segment Editor module you can segment in arbitrarily oriented slice views.
You may also choose to apply a transform to the volume that aligns it to standard orientation (e.g., by using ACPC transform module) and then resample it.
thank you so much for your reply.
So can I open a .nii file created in Mrtrix (with the function mrconvert) with Slicer?
I have tried to open this file with other imaging softwares (MIPAV) but it won’t allow me even though the NIFTI format is supported…
Or should i create a .nii file from all the dicom images just for 3dSlicer?
I am currently reading the documentation, but there isn’t much information on the formats supported and how to pass from one to the other…
Thanks a lot!
Slicer can read most file formats that are used in medical image computing - DICOM, nifti, nrrd, mha, vtk, etc. See complete list here: https://www.slicer.org/wiki/Documentation/Nightly/SlicerApplication/SupportedDataFormat
Hi and thank you so much again for your reply and help.
I managed to open my MRI scan file (.nii) in Slicer and I used the Module “Transform” to rotate the MRI view so that I can have a symmetrical view of all the structures.
To do this - within the “Apply Transform” field - I moved the MRI .nii file from the “Transformable” column on the left into the “Transformed” column on the right .
Then I changed the values in the Module menu “Edit” > “Rotation”. I had to change values for all three axes of rotation to produce a symmetrical view: LR, PA, IS. I then clicked on “Apply” in the “Convert” drop menu section.
Is this the option you suggested in your previous reply? Can I now save the .nii file transformed in this way? Or these are just viewing options?
I have tried to save the .nii file which I thought was now transformed (rotated) but when I try to open it with MRView for example it does not shpw any change.
I also tried to save it in a different way: in the “Convert” menu I put the .nii file as “Reference volume” and in “Output displacement field” I selected "create a new transform as “new name” and then I saved it as a .nii file. However, when I open this file in MRview for example it does not even show the brain scan…it’s a weird file. So what am I missing? What is the proper way of doing it?
I have been going through several of your tutorial videos, including creating labels for manual segmentation but I have found no information on this rotation process yet.
I have watched your tuttorial on transformations (https://www.screencast.com/t/Z6dQVjK3m), but I have not quite understood how then you produce a new .nii file with the same MRI scan in a new orientation.
You suggested previously to use the ACPC transform module, but I cannot find this ACPC transform among the optios. Is there any documentation I can read about this?
Resampling means that the software creates a new .nii file as a new “MRI scan” with the transformation applied to it, is that right? How do I resample it in Slicer?
Could you guide me through this process a bit more? Or is there any other tutorial that I could follow?
Thank you a lot for any help you could provide! I would really appreciate some further guidelines or link to more in-depth documentation.
Thanks a lot!