I think you need the ‘eddy’ patch to get the --data_is_shelled option in ‘eddy’ itself (or wait until the next FSL release).
Then we need to modify the HCP Pipelines to support passing in of the --data_is_shelled option in a convenient fashion. Tim Brown can comment, but I believe that will be part of the next HCP Pipeline release. 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: Sung Yu <[email protected]<mailto:[email protected]>> Date: Monday, October 3, 2016 at 11:37 AM To: Peter Kochunov <[email protected]<mailto:[email protected]>>, Michael Harms <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, Timothy Brown <[email protected]<mailto:[email protected]>>, "Glasser, Matthew" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] HCP question. Data not shelled eddy_openmp nor eddy_cuda command from fsl5.0.9 doesn't have --data_is_shelled option. --data_is_shelled: Option doesn't exist! do we have to wait for the next Pipeline release? thanks, Sung >>> "Harms, Michael" <[email protected]<mailto:[email protected]>> 9/29/2016 >>> 10:38 AM >>> See the wiki page for ‘eddy’: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/EDDY/UsersGuide#A--data_is_shelled -- 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]<mailto:[email protected]> From: Peter Kochunov <[email protected]<mailto:[email protected]>> Date: Thursday, September 29, 2016 at 9:36 AM To: "Harms, Michael" <[email protected]<mailto:[email protected]>> Cc: "Glasser, Matthew" <[email protected]<mailto:[email protected]>>, Sung Yu <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, "Brown, Tim" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] HCP question. Data not shelled Hi Michael, Do we know what this error is refering to? thanks pk On Thu, Sep 29, 2016 at 7:34 AM, Harms, Michael <[email protected]<mailto:[email protected]>> wrote: Assuming that you meant DiffusionPreprocessing, I believe that the next Pipeline release will include the capability to pass the --data_is_shelled option up onto ‘eddy’, which is what it sounds like you need for your particular data. Tim can comment on when that will be ready. 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 63110 Email: [email protected]<mailto:[email protected]> From: <[email protected]<mailto:[email protected]>> on behalf of "Glasser, Matthew" <[email protected]<mailto:[email protected]>> Date: Wednesday, September 28, 2016 at 9:10 PM To: Sung Yu <[email protected]<mailto:[email protected]>>, Peter Kochunov <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] HCP question. Data not shelled I’m not sure I understand how eddy is being run from an fMRI pipeline… Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Sung Yu <[email protected]<mailto:[email protected]>> Date: Wednesday, September 28, 2016 at 12:10 PM To: Peter Kochunov <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] HCP question. Data not shelled hi, i installed HCP pipeline v3.8.0, workbench-linux64-v1.1.1, and FSL 5.0.9 and i am trying to run the GenericfMRIVolumeProcessingPipelineBatch.sh and getting this error message: Data not shelled. terminate called after throwing an instance of 'EDDY::KMatrixException' what(): KMatrixException: msg=MultiShellKMatrix::SetDiffusionPar: Data not shelled /home/tomcat/backup/Pipelines-3.8.0/DiffusionPreprocessing/scripts/run_eddy.sh: line 258: 97798 Aborted (core dumped) ${eddy_command} it is running eddy_cuda command. Any suggestions on this issue? thanks, Sung _______________________________________________ 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. 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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. ________________________________ 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
