See my response to his question. It should work if you have the latest version of master with MSM v2 and everything is installed.
Peace, Matt. From: "Sanchez, Juan (NYSPI)" <[email protected]<mailto:[email protected]>> Date: Tuesday, January 9, 2018 at 11:24 AM To: Timothy Hendrickson <[email protected]<mailto:[email protected]>>, 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 I was having the same problem with the 3_22 FreeSurfer2CaretConvertAndRegisterNonlinear.sh and was able to download the msm binaried and the params file from https://www.doc.ic.ac.uk/~ecr05/MSM_HOCR_v1/ however I am runinng into a problem with the script at ${MSMBin}/msm --levels=4 --conf=${MSMBin}/allparameterssulcDRconf --inmesh="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii --trans="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii --refmesh="$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii --indata="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sulc.native.shape.gii --refdata="$AtlasSpaceFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii --out="$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}. --verbose cd $DIR cp "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.HIGHRES_transformed.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii The HIGHRES file does not exist. ________________________________ From: [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> on behalf of Timothy Hendrickson <[email protected]<mailto:[email protected]>> Sent: Tuesday, January 9, 2018 12:11:20 PM To: Glasser, Matthew Cc: [email protected]<mailto:[email protected]> Subject: Re: [HCP-Users] Resting State processing ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails. 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]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
