Hi All,

I am trying to run a voxel to voxel analysis comparing groups of subjects pre and post drug infusion. 53 subjects with two scans each. CONN version 17c.

The de-noising step gets stuck at step 6/6 (updating analysis variables) and I get the following message in Matlab:

"Not ready to process step conn_process_9
Saving file. Please wait...Done"

The first level analysis won't proceed without completion of this step.

I am running on a Mac server with a quad core and 32 GB of RAM and 8TB of memory to spare.

From the prior posts with similar errors it seems my RAM may be too low.

Alfonso alludes to some settings that can be changed in the conn.mat file to render this process less memory intensive.

Can anyone suggest what those might be?

Thank you!

Phil

Have you checked whether MATLAB has memory consumption limits? You can turn off java with the -nojvm flag when starting up matlab from a terminal prompt to reduce memory consumption by MATLAB.

More info here: https://www.mathworks.com/help/matlab/matlab_prog/resolving-out-of-memory-errors.html

>
> When I try this, I am unable to launch conn. Perhaps this is an issue with
> my version of Matlab? But if there are other suggestions, I would be most
> grateful.
>

Ah yes, CONN's GUI relies on Java. If you're having memory issues you can try running the CONN analysis steps interactively using the conn_batch function. Type 'help conn_batch' for more info. There are also a few example scripts included within conn itself:

- conn_batch_humanconnectomeproject.m
- conn_batchexample_singlesubject.m
- conn_batch_workshop_nyudataset

I hope this helps! Not too sure about how the MATLAB version would effect things.

Hi Phil,

You should be perfectly fine with the amount of memory in your system. I believe this error message is more likely related to not having fully gone through the previous Setup procedure. Please make sure first in the Setup.Options tab that the at least the voxel-to-voxel analyses checkbox is checked (as well any other analysis that you may want to run in the future), then click on 'Done' and 'Start' (keeping the default 'overwrite existing results' option there), and then go to the Denoising tab and do the same (click on 'Done' and 'Start'). If you are still getting the same error message please copy and paste the entire contents of the Matlab command-line window that were produced during these two steps (it should start with "CONN: RUNNING SETUP STEP") to see if that helps me figure out what might be going on here

Best
Alfonso
Originally posted by Phil Corlett:

Dear Alfonso,

We tried running the analysis again - focusing on the set-up as you described.

We ran into the same error (see attached also).

Do you have any insights?

Any suggestions would be much appreciated.

With all best wishes,

Phil

Dear Alfonso,

We are still stuck with this analysis. We set it up as you described (please see attached screen shots), and the denoising step fails every time.

Can you please check our set up and perhaps make any suggestions?

Many thanks!

Phil Corlett

Dear Phil,

Thanks for sending the detailed info. That allowed me to actually replicate your error condition, which turned out to be a bit peculiar (if I got it right). To fix your issue for now (until I create a more permanent fix) please go back to the Setup.Options tab, and in there simply follow this sequence: 1) enable the 'ROI-to-ROI' analyses; 2) disable the 'Dynamic Circuits' analyses; and 3) disable again the 'ROI-to-ROI' analyses. After this you should be able to re-run your denoising and subsequent steps without any issues. Please let me know if you still run into any problems

Best
Alfonso


Originally posted by Phil Corlett: