Re: [HCP-Users] requirements for HCP pipeline?

Thanks to everybody, you are being very helpful. Much appreciation. ___ Marta Moreno-Ortega, Ph.D. Postdoctoral Research Fellow Division of Experimental Therapeutics New York State Psychiatric Institute Department of Psychiatry Columbia University College of Physicians and Surgeons

Re: [HCP-Users] probably obvious question, but . . .

You’ll want to make sure you’re using the latest version of the main HCP public release, rather than tutorial data. You can run wb_command -cifti-correlate to compute functional connectivity from the dense timeseries data. If you want to combine across runs, you should demean the data first

[HCP-Users] probably obvious question, but . . .

Hi all, I have run the tutorial data through the HCP pipelines (v.3.4.0), but I wish to further process the resting state data. I am not sure how to proceed, however. The preprocessed data are in two places (Pipelines_ExampleData/100307/rfMRI_REST1_RL{LR}, and

Re: [HCP-Users] probably obvious question, but . . .

You don’t need to rerun ICAFIX, the HCP has already done that for you in the cleaned packages. If you want to check over the classification results, you can download the extended packages. Note I didn’t actually state an opinion for or against on global signal regression there, so if you

Re: [HCP-Users] probably obvious question, but . . .

Fair enough. And the movement signal regression? From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Thursday, February 05, 2015 11:31 AM To: Hoptman, Matthew; 'hcp-users@humanconnectome.org' Cc: Elam, Jennifer Subject: Re: [HCP-Users] probably obvious question, but . . . You don't

[HCP-Users] PBS vs fsl_sub in CHPC cluster

Hi, I’m starting to use HCP Pipelines in the WashU CHPC cluster, and got a bit confused on the way jobs are submitted to it, so I’d like to confirm a few details about this. As far as I could tell, since the cluster takes PBS jobs, and because fsl_sub works only in Sun Grid Engines(?), the way

Re: [HCP-Users] PBS vs fsl_sub in CHPC cluster

I contacted Malcolm at the CHPC to ask about this already, and he told me that fsl_sub had been somewhat customized. Yet, when I tried to execute the scripts without the —runlocal option, I got an error and the job was stopped. I guess i’m trying to figure out if the —runlocal flag is the best

Re: [HCP-Users] PBS vs fsl_sub in CHPC cluster

This might be a better question for the mailing list of this specific cluster, but I believe the version of fsl_sub on the Wash U cluster still works with PBS (I helped modify it to do this some years ago). Peace, Matt. On 2/5/15, 11:48 AM, Ramirez San Martin, Carolina

Re: [HCP-Users] PBS vs fsl_sub in CHPC cluster

fsl_sub should work with our cluster via PBS in almost all cases* Perhaps the authors of the PreFreeSurferPipelineBatch.sh script could comment on what the -runlocal flag is intended to do and whether it's been tested on our cluster? Malcolm *it doesn't properly support submitting to the GPU

Re: [HCP-Users] PBS vs fsl_sub in CHPC cluster

Hi Carolina, In the example scripts provided with the HCP Pipelines, the --runlocal flag is intended to be an indication that you do **not** want to submit a job to a scheduler or grid engine (whether PBS or SGE). If you specify the --runlocal command line option when invoking one of the example

Re: [HCP-Users] PBS vs fsl_sub in CHPC cluster

Hi Tim, that answers my question. I wondered if that '—runlocal’ option forced running the program in the cluster's login node or if it would still accept PBS job options. I’ll change the queuing_command variable then. As a new user of Pipelines and the cluster this has been the only confusing