Hi Alfonso and forum,

I am running 50 subjects in parallel using a batch script. I keep on receiving the error below. I saw there was a patch provided for an older version of conn (at https://www.nitrc.org/forum/message.php?msg_id=19218), but I'm not sure how useful it would be.

ERROR DESCRIPTION:

Error using conn_process (line 880)
duplicated ROi name atlas.FP r (Frontal Pole Right)

Error in conn_process (line 16)
  case 'setup', conn_disp([CONN: RUNNING SETUP STEP']); conn_process{[0:4,4.5,5]);

Error in conn_jobmanager (line 783)
  conn_process(job(n).fcn,job(n).args{2:end});

Do you know of any solutions?

Thank you in advance,

Georgia

Dear Alfonso and others,
I am running a batch script and I am getting the same error as below.
I have substituted the version of rex.m previously patched for CONN17, but this has had no impact on this error.

Can anyone explain what is happening here, and how it can be fixed?
Unfortunately the previous discussion of the issue is somewhat abstract and the error log does not highlight where in rex.m the error might be occurring.

From the previous discussion, I see that this is a possible culprit (quoted from here: https://www.nitrc.org/forum/message.php?...):
"Thanks for reporting this and for all the additional info, and sorry for the extra trouble (if I got it right it was a somewhat strange interaction with other settings; e.g. if you unchecked in Setup.Options the 'create REX files' option it would have worked just fine)."

Does this mean that if I set batch.Setup.outputfiles=[0,0,0,0,0,0]; this will not occur? Given that I don't set any options for Setup.outputfiles, and the help indicates that this defaults to all 0s, I am confused.

Any suggestions would be extremely gratefully received, as this issue has me completely stumped.

Thanks in advance,
Alexis

Originally posted by Georgia Gopinath:

Hi Alexis,

That error message indicates that an ROI named "atlas.FP r (Frontal Pole Right)" appears to be defined twice in your project Setup information. That particular ROI is just the first region defined within CONN's default Harvard-Oxford atlas.nii file, so my guess here is that if you go to Setup.ROIs you will find there two ROIs named "atlas" and both pointing to the same .../conn/rois/atlas.nii file. If that is the case, simply removing one of those should fix this issue.

Hope this helps
Alfonso

ps. I do not know the details of your batch script but I imagine one possible fix might be removing, if it is there, the "batch.Setup.rois.add=1" portion of it so that CONN interprets your ROIs as the explicit list of all ROIs in your project instead of as a list of some additional ROIs to be added to CONN's default ROIs (or other ROIs that you may have already defined in your project)? 


Originally posted by Alexis Hervais-Adelman:

Hi Alfonso,

thank you for your response.
I figured that this was the nature of the problem, but I couldn't work out how or why the atlas was being duplicated. Because I have over 90 data sets I prepared the batch programatically and submitted it to conn_batch. Somewhere after that oint, the number of atlases multiplied.

I was defining only the default atlases (i.e. batch.Analysis.sources={};). Although I define this value only once (i.e. not per subject), somehow this field was filled by the conn_batch procedure with the standard set of rois plus one additional entry of 'atlas' per participant in a single long list. Maybe I should have defined the field differently.

In the end though I gave up seeking the source of the error and I hacked together a simplistic solution, I just added some code conn_process to ensure there are no duplications in the roi list:
CONN_x.Setup.rois.names=unique(CONN_x.Setup.rois.names,'stable');

This may not be the tidiest solution, but it appears to be working.
Would it be desirable to implement such a feature in the release, or have I set myself up for some kind of mishap in future?

Thanks again, and best regards
Alexis

Originally posted by Alfonso Nieto-Castanon: