Questions about dpabisurf preprocessing error

Submitted by DHLee on

Hi, prof. Yan.

I have several questions about dpabisurf preprocessing. 

I performed dpabisurf preprocessing  for 10 subjects(PreAcuS001-S010). 

At first, I thought it was going well, but an error occurred and dpabisurf stopped working(attached photo).

Perhaps the problem occurred during the process of fmriprep

And It seems that an error occurred during the segmentation of one subject(S008)

I checked the error message only today after the weekend, and  it seems to have failed despite re-running fmriprep several times automatically in the dpabisurf.

I am not exactly sure but, it doesn't seem to be any problem visually in the T1 raw image(nii file) of the subject. 

In this situation, I have two questions. 

1. In this case, How should I proceed to solve the problem? (segmentation...) 

2. Except for the problemed subject, fmriprep seems to have worked well for the rest of the subjects(other 9 subjects). However, the dpabisurf pipeline stopped.

If I want to continue the rest of the preprocessing steps(without start over again from initial FunImg/T1Img) on 9 subjects that have progressed well, how should  I start? 

(at first, I checked after fmriprep(from organize fmriprep-Nuisance covariate regression-...- smooth derivates), but I don't know the 'Starting Directory Name'(ex. FunRaw, FunImg))

I look forward to your wise comments. 

Sincerely, Thank you. 










YAN Chao-Gan

Fri, 05/13/2022 - 10:46

I think there is something wrong with the raw data for this subject.

Starting Directory Name is "fmriprep", and then check the Organize fmriprep results. On the subject list, right click and remove the failed subject. Then that should be fine.