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

1

Hi,

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.

INU_uncorrected
INU_uncorrected.jpg1830×784 299 KB

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.

T1-segmentation
T1-segmentation.jpg1826×776 584 KB

P.S I have tried to change the multiple output spaces in 1.4.0 version as well:

–output-space T1w template fsaverage

versus

–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.

Bests,

T

2

Hey guys, we were looking at the results again today and it looks like maybe the INU correction is working (because all the brain masks and MNI alignment looks much better now) but the QA report are building the screenshots from the non-INU corrected images. Is this the case?

@oesteban @effigies ?

3

This has been bugging me for a long while now but I keep forgetting opening an issue. Could you force me to check on this submitting a new issue?

(yes, you are right, the reports are probably showing uncorrected images).

4

Testing a solution for this in https://github.com/poldracklab/smriprep/pull/102