Fmriprep V1.4.0 does not correct for INU and generate a full html report



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


–output-spaces MNI152NLin2009cAsym
–skull-strip-template MNI152NLin2009cAsym

The problems I mentioned above still stand. Sorry for the long post, but I am desperate in need of helps.