January 22, 2016 at 1:13 am #199
I’m interested in running this script.
I have same questions before:
– How can I co-register final results with an Anatomical Template (for example ICBM152)?
– How can visualize it in brainsuite?
January 22, 2016 at 8:49 pm #203cbhushanModerator
1) what set of results/files do you want to transfer to the template? In general, you would need to perform a registration between the subject files and template files. If you have already processed your T1 data with SVReg (and BrainSuite extraction) then results can be transferred to the BrainSuite template. If you want to transfer to ICBM then you would need to perform an affine registration with register_files_affine tool (or any other tool of your choice).
2) Visualization can be done in Brainsuite itself.
3) mergeDWIs and register_files_affine are matlab functions and has to be used from through matlab. Details and examples of these functions are available at http://neuroimage.usc.edu/neuro/Resources/BDPAddons
January 25, 2016 at 2:09 am #206
I’m interested in merge multiple DWI from different subjects (all subjects aquired in the same way!)
Then I would like to reconstruct merged_DWI in a single template (like ICBM 152) and finally vizualite it in brainsuite.
I already merged 7 DWIs from different subjects, then I processed BDP_15c for the merged_DWIs without –no-structural-registration. I run the results in BS_15c but it looks like absolutley not good, full of noise. Do you have any suggestions?
January 25, 2016 at 9:58 am #207cbhushanModerator
Hi Luca, Probably it is not clear from the documentation of mergeDWIs, but mergeDWIs does not perform any type of registration or alignment across DWIs. It literally just concatenates one DWI volume after another and is written for a different use case (where diffusion dataset from same subject is somehow split into multiple files, either by the scanner or because of the way data was acquired).
From your last answer, it seems that you are interested in studying the group average diffusion properties. Is that correct? If so, then you would need to co-register the subjects to the template and then transfer the subject data to the template. This can be done in most straight-forward fashion if you first run BDP in the native space (i.e. run BDP separately for each subject in usual fashion) which will give you diffusion properties like FA, MD etc in the native-space of each subject. Then you can use affine/non-registration to transfer these diffusion properties to the template and look at statistics like mean, variance etc. If you want use BrainSuite template then running SVReg on your subject’s T1w data would the recommended way. If you want to use ICBM template then you would need to register each of the subject to the template and transfer FA/MD/others (using register_files_affine or other tool of you choice).
January 26, 2016 at 1:40 am #208
Yes you are correct, I’m interested in studying the group average DWI.
Do I need to use register_affine_files and coregister all my DWIs.nii (moving_filename) to BrainSuite Template (statict_filename)?
Finally How can I merge co-register DWIs to template in one averaged DWI?
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