If you’re talking about some sort of community/modularity analysis, then, no, there aren’t any tools for doing that directly in workbench.
Maybe Tim C. will have some suggestions. I believe that the dconn is stored as a single precision float. Have you tried using ‘ciftiopen’? I’m not sure if that preserves the single precision format of the data, or if it balloons by a factor of 2 due to conversion to matlab’s default double precision format. If you can keep it as single precision in matlab, you might be able to work with it provided Matlab has access to a lot of RAM. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [email protected] From: "GLOMB, KATHARINA" <[email protected]<mailto:[email protected]>> Date: Tuesday, October 25, 2016 at 10:35 AM To: Michael Harms <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Problem with handling dense FC matrix Hi Michael, wow, thank you for this lightning speed reply! I want to run some network analysis on this matrix.I don't need the whole matrix, I would just need the unique entries (off-diagonal upper or lower triangular, squareform() in Matlab) - maybe that would help? Can workbench help me in any way to do this? Or do you have any other ideas? Thank you! Katharina On Tue, Oct 25, 2016 at 5:21 PM, Harms, Michael <[email protected]<mailto:[email protected]>> wrote: What are you trying to do with the file in workbench? Have you reviewed the tutorial, because it includes examples (and a scene to help you along) of using that file. Trying to load/work with that file in matlab is probably going to cause loads of pain. It is just too large to load the entire thing into matlab. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173<tel:314-747-6173> St. Louis, MO 63110Email: [email protected]<mailto:[email protected]> From: <[email protected]<mailto:[email protected]>> on behalf of "GLOMB, KATHARINA" <[email protected]<mailto:[email protected]>> Date: Tuesday, October 25, 2016 at 10:15 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Problem with handling dense FC matrix Hello HCP users, I am new to HCP so please excuse me if I'm asking something that should be obvious. I've tried to find a solution but haven't been successful so far. I am trying to use the file HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii which to my understanding should contain a full FC matrix that is an average of 820 subjects. I want to feed this matrix into a Matlab function. Of course, this is problematic because of the memory requirements. I have tried to read the file using ft_read_cifti from fieldtrip, but Matlab crashes at 112 GB of memory. So clearly, this is not the way. I know I am supposed to be able to use workbench for that, but can't make it work so far. Can someone point me in the right direction? Is what I'm trying to do impossible? I am using a cluster that can handle up to 132 GB of memory per cpu (RAM+swap) and runs Debian. Thank you!! Katharina -- PhD candidate<http://www.cns.upf.edu/katharina> Computational Neuroscience Group<http://www.cns.upf.edu/> Center for Brain and Cognition<http://cbc.upf.edu/> Universitat Pompeu Fabra<http://www.upf.edu/> Barcelona, Spain I am funded by the INDIREA<http://www.indirea.eu/> Marie Curie Initial Training Network. _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -- PhD candidate<http://www.cns.upf.edu/katharina> Computational Neuroscience Group<http://www.cns.upf.edu/> Center for Brain and Cognition<http://cbc.upf.edu/> Universitat Pompeu Fabra<http://www.upf.edu/> Barcelona, Spain I am funded by the INDIREA<http://www.indirea.eu/> Marie Curie Initial Training Network. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
