Fixel based analysis in MNI space

1

Dear Experts,

I have conducted FBA on my subject data and extracted FA images using MRtrix. After aligning the FA images to MNI space, I performed SPM’s TFCE analysis in MATLAB.

I would like to ask: if I want to compare the results of FBA with the results from SPM, would it be better to align the subject data to MNI space before running FBA, or should I align the wmfod_template.mif to MNI space instead?

Currently, I have adopted the second approach: aligning the wmfod_template to MNI space. I then followed the official tutorial to complete the subsequent FBA steps. However, I got stuck at Step 19, where I couldn’t proceed with tcksift. Could you please advise me on which part of my steps needs adjustment?

And these are the commands I’ve done to aligning wmfod_template to MNI space:

fslmaths ../wmfod_template_l0.nii.gz -nan l0image.nii.gz
flirt -ref ../../../JHU/MNI152_T1_1mm_brain.nii.gz -in l0image.nii.gz -out l02MNI.nii.gz -omat l02mni.mat
fnirt --ref=../../../JHU/MNI152_T1_1mm_brain.nii.gz --in=l0image.nii.gz --aff=l02mni.mat --cout=warps_l02mni
ls
warpinit l0image.nii.gz identity_warp_wmfod_template.nii
applywarp --ref=../../../JHU/MNI152_T1_1mm_brain.nii.gz --in=identity_warp_wmfod_template.nii --warp=warps_l02mni.nii.gz --out=mrtrix_warp_template2mni.nii.gz
ls
mrconvert identity_warp_wmfod_template.nii -coord 3 0 - | mrcalc - 0 -mult 1 -add identity_warp_wmfod_template_mask.nii 
applywarp --ref=../../../JHU/MNI152_T1_1mm_brain.nii.gz--in=identity_warp_wmfod_template_mask.nii--warp=warps_l02mni.nii.gz --out=mrtrix_warp_template2mni_mask.nii.gz
applywarp --ref=../../../JHU/MNI152_T1_1mm_brain.nii.gz --in=identity_warp_wmfod_template_mask.nii --warp=warps_l02mni.nii.gz --out=mrtrix_warp_template2mni_mask.nii.gz
ls
mrcalc mrtrix_warp_template2mni_mask.nii.gz 1 nan -if mrtrix_warp_template2mni.nii.gz -mult mrtrix_warp_template2mni_valid.nii.gz
mrtransform ../wmfod_template.nii.gz -warp mrtrix_warp_template2mni_valid.nii.gz -template ../../../JHU/MNI152_T1_1mm_brain.nii.gz wmfod_template_MNI.nii.gz -reorient_fod yes
mrinfo wmfod_template_MNI.nii.gz

Here is the error in tcksift:

image
image883×308 81.1 KB

Best,
Vivian

2

Hi Vivian,

Maybe it is a typo, but running Fixel-Based analysis on your subject would result in Fiber Density maps rather than Fractional Anisotropy maps. You could achieve FA maps by dwi2tensor and tensor2metric. By running SPM’s TFCE I actually assume you’ve acquired FA maps, since FBA statistical analysis requires connectivity-based fixel enhancement and cannot be done with SPM.

Moreover, regarding aligning a subject-space dMRI to MNI, it will result in fibers not being aligned anymore. FBA pipeline ensures that fiber orientation information is preserved even if the subjects are resampled to the subject-level group template - but if you’ve done FA analysis, you can simply do a non-linear registration of FA maps to MNI. See TBSS.

Also, considering your weird SIFT log, I would do the quality control checks for all the pipeline.

Best,
Amir

3

Dear Amir,
Thanks for your response. Maybe there are something wrong with my explanation.
After performing TFCE in SPM with FA images and performing FBA with fdc images, I got both the analysis results. I want to view them in same space. So, I tried to register wmfod_template.mif to MNI space and execute FBA again. The error message is in the tcksift step.

Sincerely,
Vivian