To further explain: "latest master" means you should *not* go to the "releases" page on github. Instead, go to the main page, https://github.com/Washington-University/Pipelines , and click the green "clone or download" button on the upper right above the file list.
Tim On Tue, Jan 9, 2018 at 11:25 AM, Glasser, Matthew <[email protected]> wrote: > 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]> > Date: Tuesday, January 9, 2018 at 11:24 AM > To: Timothy Hendrickson <[email protected]>, Matt Glasser < > [email protected]> > Cc: "[email protected]" <[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/ > <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] <hcp-users-bounces@ > humanconnectome.org> on behalf of Timothy Hendrickson <[email protected]> > *Sent:* Tuesday, January 9, 2018 12:11:20 PM > *To:* Glasser, Matthew > *Cc:* [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 <(612)%20624-6441> > Mobile: 507-259-3434 <(507)%20259-3434> (texts okay) > > On Mon, Jan 8, 2018 at 7:16 PM, Glasser, Matthew <[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]> > Date: Monday, January 8, 2018 at 9:15 AM > To: "[email protected]" <[email protected]> > Cc: Matt Glasser <[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 <(612)%20624-6441> > Mobile: 507-259-3434 <(507)%20259-3434> (texts okay) > > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
