Yes, that’s all you have to change!
Hi, sorry for the late reply, I followed your advice and subject-29576 can be preprocessed perfectly, however, when I apply the same pipeline to other subjects, although the CSF file is alright the ‘ValueError: Number of time points’ still remains.
Below is the CSF mask result:
And here is the log files:
pypeline.txt (361.7 KB)
29542_pypeline.txt (362.5 KB)
29576_pypeline.txt (809.7 KB)
29577_pypeline.txt (362.3 KB)
Could you please help me to find out which part goes wrong?
Thank you for your time!
After running some tests, it looks like the lateral ventricle mask may be too stringent for some of the subjects, which is why this error appears to be data dependent. The error disappeared when I ran this pipeline without the lateral mask. Omitting the mask would be a less conservative approach to extracting the CSF mask, but it seems like it isn’t compatible with the dataset. You can just replace the path to the mask with None. Let me know if you have any questions!