Hi Saad,
I have re-checked my data and found the problem you were talking about-- my parcellation (find_the_biggest) maps are cut-off because the fdt_paths datasets either do not completely cover my standard MNI template (or my seed ROIs) or they are off-set somehow.
I checked with the original data.nii.gz files and after converting them to MNI space using FLIRT, they are correctly aligned and cover the entire MNI surface when overlayed on a standard template.
I can only think that the error is being produced during the FDT registration step (where I use the same MNI template as my "standard" space), but am not sure what I'm doing wrong. I input the correct Bedpostx directory, a structural image, and the MNI152_T1_2mm standard template, and use all the default setting (normal search, 12 DOF, and correlation ratio). Then for probtrackx, I specifically use the standard2diff.mat file as my xfm.
Do you have any suggestions as to why my fdt_paths are not aligned to the MNI template properly?
Thank you for your help!
Samantha
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