I am trying to do DTI analysis suing FSL software. But since MNI152 is related to human brain. How do I register a pig brain atlas and use it to tbss analysis.
I have used tbss_2_reg -t
the tbss_3_postreg -S but after this when I viewed the mean_FA some of the part got canceled out
Hi @Sanjida and welcome to neurostars!
You might find the script in $FSLDIR/etc/xtract_data/standard/F99 helpful. It is for macaques, but you can replace the relevant standard space with that for pigs, e.g., ( https://doi.org/10.1101/2020.10.13.337436). See more here: XTRACT - FslWiki
Best,
Steven
Hi Steven,
Thank you so much for your response.
I have an atlas for pig from UIUC and I am using TBSS reg process (Nonlinear Registration). But although I am using my own template it seems not to be working. XTRACT command say before running it we must complete FDT pipeline which includes Nonlinear registration. How do I use the altas or PNI152 template instead of MNI152 as the FSL automatically take that in account.
Thank you so much!
Sanjida
Hi @Sanjida,
In what ways did you change the helper registration script and what errors did you get?
Best,
Steven
Hi,
So, for TBSS ANALYSIS, at first used tbss_2_reg -t (where I specified my target image)
THEN. after the tbss_3_postreg -S ( brain cell got skipped out after results was viewed)
How do I register the atlas as an standard space in FSL which I can use further)
Best,
Steven
Did you look at the the script I mentioned in my earlier answer (/$FSLDIR/data/xtract_data/standard/F99/do_reg_F99.sh)? I imagine you can replace some of the files referenced in that script with those from your own atlas, albeit I do not know what files your atlas has.
it has just the atlas and FA map in NIFTII form if that is what you meant.
so Instead of F99 can I add my file then.
Looking at the script, I think the only file that is used is mri/struct_brain in the f99dir argument (which is the third positional argument to the script).
Hi steven,
Another help please, in FSL the from the pig’s brain view I can see the axes are nor correct. For example, which is supposed to be the superior side, it is showing as anterior side of the brain. Moreover, the fslview are correct about the pig brain’s sagittal axial and coronal view. May be because during the MRI scan the pig brain positions are not same as Human. How do I correct and specify right name for the axes and for the side for the brain.
Hi @Sanjida,
Are the labels correct but just not displayed on the conventional side? That is, even if it looks different than normal, is the anterior side still labeled as anterior? If so, you can reorient with fslreorient2std. Otherwise, it gets complicated as described here: Orientation Explained - FslWiki
Best,
Steven
@Sanjida I would check each step of your analysis when processing DTI data from a quadruped. Each MR manufacturer reports their gradient directions differently, and most tools in our community use the FSL/BIDS format for bvectors which requires gradient directions to be reported in image space, not world space. There are lots of opportunities for conversion errors from the tools or the operators (e.g. prone or supine imaging). I would suggest you read the validate DTI vectors document and use FSLeyes to view vectors. You may also want to see if GradFlipTest improves the performance.
No I believe, the side that is supposed to be the anterior side is labelled as superior side of the for the pig brain. Also the sagittal, coronal and axial views are kind of different for the fslview of our pig brain and the atlas one. If I am not wrong the sagittal, axial, coronal view should be same for all brain no matter how the MRI scan is done? or it is beacuse in FSL all of them are compared with MNI space and that changed the pig brain orientation. Does the orientation or the axes going to affect the analysis in future. Do we need to change axes and orientaion.
This orientation issue is indeed a tricky issue. I see that often happening due to the fact that the individual is registered at the MRI console in a certain way, let’s say head first - supine and the subjects is eventually in a different position (sphinx position for instance).
It was discussed here with some solutions proposed for anatomical images:
When diffusion MRI is involved, it gets even more tricky as @neurolabusc is saying: you have to taken into account also the gradient directions. Among the tools listed by @neurolabusc to help you check those orientations, I would add the dwigradcheck tool.
The procedure is given in this thread from the mrtrix forum:
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