How to continue halted preprocessing?

Submitted by puyunfashi on

DPARSFA and DAPBISurf are two “pipelines,” meaning they consist of several steps. After encountering a bug during preprocessing, it would be handy to continue the preprocessing from the step where it was halted. DPARSFA/DPABISurf does preprocessing from left to right and top to bottom on GUI. So, continuing preprocessing contains the following steps: 

1) Close the halted DPARSFA/DPABI GUI; 

2) Open a new DPARSFA/DPABI GUI; 

3) Uncheck all the finished steps. The finished ones can be told by the “Tips for Starting Directory Name” pop-up window, which can be seen by hitting Return after deleting the default value (“FunRaw”) in the Starting Directory Name box. You may look at the existing folders in the current working directory. Please note that the latest folder might be empty. So, the finished steps can be determined by the latest non-empty folder;

4) input the latest finished folder name into the Starting Directory Name box and TR info into the TR (s) box, then hit Run.

 

DPARSFA

Next step

Starting Directory Name

Notes

Slice timing

FumImg

The dicom to nifti step and removing first x time points step can not be separated as two steps;

Realign

FunImgA

 

Reorient

FunImgAR

 

Bet

FunImgAR

 

T1 Coreg to Fun

FunImgAR

 

New Segment + DARTEL

FunImgAR

 

Nuisance Covariates Regression

FunImgAR

 

Normalize

FunImgARC

 

All default metrics

FunImgARCW

I personally suggest leave the default metric setting as they were and simply re-run all metric calculation altogether. You would not need to worry about some tricky settings for some metrics (e.g., ALFF/ReHo) and calculating all metrics won’t cost too much time whatsoever.

Functional connectivity/Extract ROI time courses

FunImgARCWF

Probably the most frequently used re-run setting. I personally recommend run these two steps at the same time. Uncheck all the rest steps first.

 

DPABISurf

Next step

Starting Directory Name

Notes

Convert to BIDS

FunImg

 

Preprocessing with fmriprep

BIDS

From my understanding, slice timing is coupled with Preprocessing with fmriprep

Organize fmriprep

fmriprep

 

Nuisance Covariates Regression

FunSurfW

 

All metrics

FunSurfWC

 

Functional connectivity/Extract ROI time courses

FunSurfWCF

 

Attachment Size
Where are Starting Directory Name and TR (s)? 202.89 KB
Where are Starting Directory Name and TR (s)? 190.02 KB
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DPABI/DPABISurf/DPARSF