Hello,
I registered T1 with lesion in standard space MNI, I using flirt and fnirt, the output of T1-registration and the mask-registration has wavering effect from one slice to another, is there any reason why that happens and a solution to the problem?
I tryed two tests:
1. the data inserted in Flirt and Fnirt are isotropic 1x1x1 and once I registered T1 it didn't seen to have any problem but the registered mask had an intensity of less than 1 on the edges.
Commands
flirt -in T1file -ref T1file -out xxx -applyisoxfm 1
fnirt --ref=MNI152_T1_1mm --in=T1file --inmask=invmask --aff=matrix --iout=xxx --fout=xxx
applywarp -i file -o xxx -r MNI152_T1_1mm -w filebyfout --interp=nn
2.the data I addition to the first attempt I added the interpolation nn command to the command that makes isotropic data 1x1x1 but a problem comes up, when I register the T1 and the mask i get a wave effect (making from one slice to the other).
Commands
flirt -in T1file -ref T1file -out xxx -applyisoxfm 1 -interp nearestneighbour
fnirt --ref=MNI152_T1_1mm --in=T1file --inmask=invmask --aff=matrix --iout=xxx --fout=xxx
applywarp -i file -o xxx -r MNI152_T1_1mm -w filebyfout --interp=nn
Thank you for your help
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