There are several issues I would like to address here:
1. I have tried to use the new fmriprep (1.4.0) which included the inu_correction in the workflow, however, the output was not corrected. I will be attaching the image below.
2. The HTML report only included part of the functional data. For example,
- Subject ID: MRP0155
- Structural images: 3 T1-weighted (+ 1 T2-weighted)
- Functional series: 6
- Task: emp (3 runs)
- Task: imi (1 run)
- Task: obs (1 run)
- Task: rest (1 run)
the HTML report ended at run 3 for emp, although all the functional data are available.
3 The tissues segmentation of T1 was way off and there are lots of brain tissues missing in the image. I have read forum posts regard to this issue, and there are several T1-weighted images in this study. Are there any way to fix this.
P.S I have tried to change the multiple output spaces in 1.4.0 version as well:
–output-space T1w template fsaverage
The problems I mentioned above still stand. Sorry for the long post, but I am desperate in need of helps.