Nope, Matt, no empty EVs and estimations worked fine for subcortex with the exact same design.
Removing ‘--sa --ms=15 --epith=5’ did make it work. Any ideas what would this indicate? Moataz From: Glasser, Matthew [mailto:[email protected]] Sent: 18 June 2019 02:54 To: Harms, Michael <[email protected]>; Moataz Assem <[email protected]>; [email protected] Subject: Re: [HCP-Users] film_gls error pinv() svd() Is there anything weird about your design like empty EVs? Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "Harms, Michael" <[email protected]<mailto:[email protected]>> Date: Monday, June 17, 2019 at 12:55 PM To: Moataz Assem <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] film_gls error pinv() svd() Hmmm. Assuming the problem is reproducible, I think you’ll have to report this, to the FSL list. To provide additional information, it might be helpful to hack the TaskfMRILevel1.sh script to not use the ‘--sa --ms=15 --epith=5’ flags in the call to ‘film_gls’ (or, perhaps easier, just try running the modified film_gls call directly from the command line). And if that still fails, try turning off the autocorrelation estimation entirely with the ‘--noest' flag. Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry 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]<mailto:[email protected]> From: <[email protected]<mailto:[email protected]>> on behalf of Moataz Assem <[email protected]<mailto:[email protected]>> Date: Monday, June 17, 2019 at 9:32 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] film_gls error pinv() svd() Hi, I get the following fsl error related to the beta estimations (while running film_gls): Prewhitening and Computing PEs... Percentage done: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39, error: pinv(): svd failed pinv(): svd failed This only happens for one run (in one subject) and while estimating the left surface (subcortical estimation ran fine). The design matrix doesn’t contain any NaNs neither does the timeseries for that hemisphere (also std(timeseries) did not give any zeros). I am wondering if you can suggest other problems to check for? Thanks Moataz _______________________________________________ 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. _______________________________________________ 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. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
