June 5, 2018 at 2:23 pm #1263
I noticed a resampling glitch when the dMRI is warped to a T1 with an oblique sform:
The glitch appears as one or more diagonal fault planes that are more or less conspicuous depending on the local contrast – the screenshot shown is from the worst case on the inferior edge of the CC.
The T1’s sform is
srow_x 280 4 1.195487 -0.00832 -0.0876 -85.916519
srow_y 296 4 0.029844 0.995965 0.197129 -165.741318
srow_z 312 4 0.099596 -0.198567 0.992426 -124.586205
There is no problem when the same T1 is used with sform
srow_x 280 4 1.2 0.0 0.0 -99.663498
srow_y 296 4 0.0 1.0156 0.0 -97.173988
srow_z 312 4 0.0 0.0 1.0156 -128.981201
Has anyone else seen similar problems with obliqued T1s, and is there a possibility of fixing the resampler?
June 5, 2018 at 2:25 pm #1264
June 10, 2018 at 7:00 pm #1299Anand JoshiModerator
Thanks for reporting the issue. Can you please let me know which executable were you using? Was it BDP.sh?
You can try the following workaround for now. You can simply load and save the T1 from brainsuite. It should save the header in brainsuite friendly format. Then proceed with the analysis using this saved T1.
June 18, 2018 at 2:38 pm #1331
Sorry for not replying earlier. I was using BDP.sh, for scriptability, and have never actually gotten the whole brainsuite package running. If I understand correctly though, and I think I do, I could easily manipulate the T1 to have a diagonal (non-oblique) affine matrix outside brainsuite, and carry on. I do not mind resampling the T1 for this purpose since its native resolution is much better than the dMRI’s.
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