Those files are in the pipelines: https://github.com/Washington-University/Pipelines/tree/master/MSMConfig
Version 2 of MSM is the correct one to use. It is indeed correct that you use the latest version of the HCP Pipelines with the latest version of MSM and make sure that you have installed everything correctly. MSM was not previously publicly available before this version. Matt. From: Timothy Hendrickson <[email protected]<mailto:[email protected]>> Date: Tuesday, January 9, 2018 at 11:11 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Resting State processing Hi Matthew, The file does not exist. I see now that the PostFreeSurfer pipeline I have locally is different than the latest version found on github (specifically FreeSurfer2CaretConvertAndRegisterNonlinear.sh). I see that the line referencing allparameterssulcDRconf has been commented out in favor of MSMSulcStrainFinalconf, however, this file does not appear to exist either. Which version of MSM HOCR is the most recent that should be used? I am using version 2) On a completely other note why aren't these configuration files already included in the HCP pipelines? It seems very burdensome to require each user to mimic the exact version of the MSM binaries that FreeSurfer2CaretConvertAndRegisterNonlinear.sh expects. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) On Mon, Jan 8, 2018 at 7:16 PM, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: Does the file exist? That might be the old config file it is looking for suggesting that you don’t have the latest master. Peace, Matt. From: Timothy Hendrickson <[email protected]<mailto:[email protected]>> Date: Monday, January 8, 2018 at 9:15 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Cc: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Resting State processing Hello all, Despite having the most recent version of the hcp pipeline (3.22) and downloading the MSM configuration binaries, however, I am still receiving an error when I attempt to run the PreFreeSurfer pipeline with RegName="MSMSulc". This is the error message I receive: /opt/local/hcp-pipelines-3.22.0/Pipelines-3.22.0/MSMBinaries/allparameterssulcDRconf: Couldn't open the file! -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441<tel:(612)%20624-6441> Mobile: 507-259-3434<tel:(507)%20259-3434> (texts okay) _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
