DPARSF functional connectivity error



I have the following error come at the last step of pre-processing after ROIs are being made, during functional connectivity (or even after trying the ROI making step). Any help would be appreciated! Thanks.

Error using y_ReadAll (line 60)

The input name is not supported by y_ReadAll: /Users/amrithah/Desktop/test2/FunImgARglobal/0010028
Error in y_ExtractROISignal (line 56)
    [AllVolume,VoxelSize,theImgFileList, Header] =y_ReadAll(AllVolume);
Error in DPARSFA_run (line 2500)
        parfor i=1:AutoDataProcessParameter.SubjectNum
Error in DPARSFA_RerunWithGSR (line 94)
Error in DPARSFA>pushbuttonRun_Callback (line 1789)
Error in gui_mainfcn (line 95)
Error in DPARSFA (line 30)
    gui_mainfcn(gui_State, varargin{:});
Error while evaluating UIControl Callback



It seems that you did not run covariates regression and normalize to your data? Maybe you should do all recommended preprocessing steps first.



So I reran that subject with 'normalize by DARTEL' checked, and I saw that it also performed covariate regression. I saw all outputs correctly, including functional connectivity analysis this time, but these errors came in red even after running successfully. My question is, did the pipeline run successfully after all then, or are there any more steps after that? Attached are the parameters I checked. 

Then you may try to do fc with the folder "FunImgARglobalCWF".

Hmm okay. Can I restart the pipeline from that folder? If you see my screenshot, the 'Run' button is in red, and it's frozen on that. Would I just close the terminal down, and restart it, and load that 'FunImgARglobalCWF' folder into the subject directory instead to pick it back from that point?

No need to change the working directory. You may restart the terminal and uncheck all the checkboxes on the terminal except for "functional connectivity" and "Extract ROI time courses". Don't forget to click the "Define ROI" button to define ROIs. Finally, you should change the start directory to "FunImagARCWF", then click RUN. Good luck! 

Okay I’ll give your suggestion a try! Only confusion though is my folders only go up till FunRawARCovs and FunRawARCFWS for the functional connectivity output. Am I missing something, and if so, where do I go from here? Thank you!

It ended up working thanks!!

There is something wrong with your pipeline. If you start with nifti files, you should change the start directory to "FunImg". 

The second issue is the covariates regression. I don't know why you only got the "FunRawARCovs". With common settings, you should two folders named "FunImgARglobalCWF" and "FunImgARCWF" containing results with and without global signal regression.

Anyway, I suggest you rerun your data with the default setting. Be careful, if you start with nifti files, you should change the start directory to "FunImg". 

I still don’t see the file you mentioned after rerunning it regarding the global signal regression, but the analyses all ran correctly. I am thinking I’ll just manually uncheck GSR and no GSR, but I don’t know if it’s a Mac issue. I had checked with both with and without GSR under nuisance regression and that folder still don’t show up.

Even with running GSR/no GSR separately, this is what I see (in addition to comparing it with checking 'both GSR and no GSR option')- both times, the files showed up liked:

Never mind- I changed the directory as you said and it worked perfectly. Thank you so much! Changing it to FunImg did the trick.