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open-discussion > dMRI data in the PROCESSED folder
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Feb 24, 2021 08:02 PM | Brian Jung
dMRI data in the PROCESSED folder
Hi, I have a question regarding the dMRI data in the PROCESSED
folder.
I believe the data in the PROCESSED folder is an additional step from AutoQC. Specifically, I think it is a version of AutoQC data that has isotropic voxels. You can see this on the .nii and/or .nrrd metadata. Voxel dimensions in AutoQC are ~0.65 × ~0.65 × ~1.30 mm while in PROCESSED are ~0.65 × ~0.65 × ~0.65 mm.
The main reason we are interested in using the data in the PROCESSED folder is not because of the resolution, but because it already contains a brain mask (brain segmentation). Having this mask means we don't have to deal with fibers originating in surrounding (non-brain) tissues. That would also help for future co-registration to the structural MRIs.
Unfortunately, the DTI data (tensor data) in the PROCESSED folder seems to have problems. The tractography reconstruction generated in Diffusion Toolkit makes no sense: all fibers have the same orientation (see image attached). I initially thought this was a problem on my side (that I had used wrong parameters), but others get similar results.
So did the data in PROCESSED not undergo tensor reorientation during resampling and is actually not intended for analysis? Can the data in PROCESSED can be used for analysis and tractography reconstruction? Or are brain masks available for data in AutoQC?
I believe the data in the PROCESSED folder is an additional step from AutoQC. Specifically, I think it is a version of AutoQC data that has isotropic voxels. You can see this on the .nii and/or .nrrd metadata. Voxel dimensions in AutoQC are ~0.65 × ~0.65 × ~1.30 mm while in PROCESSED are ~0.65 × ~0.65 × ~0.65 mm.
The main reason we are interested in using the data in the PROCESSED folder is not because of the resolution, but because it already contains a brain mask (brain segmentation). Having this mask means we don't have to deal with fibers originating in surrounding (non-brain) tissues. That would also help for future co-registration to the structural MRIs.
Unfortunately, the DTI data (tensor data) in the PROCESSED folder seems to have problems. The tractography reconstruction generated in Diffusion Toolkit makes no sense: all fibers have the same orientation (see image attached). I initially thought this was a problem on my side (that I had used wrong parameters), but others get similar results.
So did the data in PROCESSED not undergo tensor reorientation during resampling and is actually not intended for analysis? Can the data in PROCESSED can be used for analysis and tractography reconstruction? Or are brain masks available for data in AutoQC?
Feb 24, 2021 09:02 PM | Roza Vlasova - UNC at Chapel Hill
RE: dMRI data in the PROCESSED folder
Hi Brian,
I downloaded several DTI images from PROCESSED folder and checked them. They looks good (I attached screenshot from Slicer tool).
We don't use Diffusion Toolkit, but as I know from my experience with it - this tool supposed to reconstruct tensors from DWI images, so, you should provide preprocessed DWI images to have tensor image as output. Try to input to TrackVis DTI file directly, without Diffusion Toolkit step (because it's already tensors), if you will have problems with that, I suggest you to use files from AutoQC as input to Diffusion Toolkit. We have masks for structural data for the same subjects, you can register this masks to diffusion space.
Best,
Roza
Roza Vlasova PhD., Postdoctoral Fellow
Neuro Image Research and Analysis Lab
Departments of Psychiatry
University of North Carolina at Chapel Hill
I downloaded several DTI images from PROCESSED folder and checked them. They looks good (I attached screenshot from Slicer tool).
We don't use Diffusion Toolkit, but as I know from my experience with it - this tool supposed to reconstruct tensors from DWI images, so, you should provide preprocessed DWI images to have tensor image as output. Try to input to TrackVis DTI file directly, without Diffusion Toolkit step (because it's already tensors), if you will have problems with that, I suggest you to use files from AutoQC as input to Diffusion Toolkit. We have masks for structural data for the same subjects, you can register this masks to diffusion space.
Best,
Roza
Roza Vlasova PhD., Postdoctoral Fellow
Neuro Image Research and Analysis Lab
Departments of Psychiatry
University of North Carolina at Chapel Hill