Hello,

I'm working on rhesus monkey brain MRI analysis and I've download some images from https://data.kitware.com/#collection/54b...
But, I found that T1/T2 images have different orientation and image origins from FA/MD images.
My purpose is to co-register estimated FA/MD images to T1 image space.
I've tried to align using FSL flirt, but I was not able to do it due do background noise and skull without manual skull stripping of FA/MD images.

So, I'd like to ask you whether there are skull-stripped FA/MD images or original DICOM images are available for reprocessing.
Additionally, do you have Fiedlmap images for distortion correction?
Hope I can get some advice on rhesus monkey image analysis.
Thank you.

jeongchul.

Hi Jeongchul
We are currently manually editing the DTI brain masks and will make them public as soon as that is done (probably by June). 

Re field map: No, we did not acquire any field map.

Re DICOM: Not sure why it would be needed, as one easily convert the NRRD data to Nifti (e.g. using DWIConvert/DWIConverter in 3D Slicer). The issue with the DICOM data is that some datasets have incorrect DICOM orientation information, which we corrected.

Re FLIRT:, FLIRT won't be enough for an appropriate correction for the distortions in the diffusion data. The data has significant distortions in the anterior temporal lobe area, which need a non-linear registration (FLIRT is a linear registration tool).

Martin

Dr. Martin,

That sounds great.
Hope updated brain masks are available soon.
Thank you.

Jeongchul.