Re: [HCP-Users] Extract 137 RSN networks - Glasser et al. - Nature 2016
Sounds like it made a temporary file for some reason, but the temporary file was corrupt somehow (found a similar error on the freesurfer list). You should probably ask the freesurfer list what the problem might be. Tim On Wed, Oct 12, 2016 at 12:27 PM, Francesco Sammartino < francesco.sammartino@gmail.com> wrote: > Thank you a lot. > > I found a problem in the last step. When I convert files from gii to annot > using mris_convert : I run mris_convert --annot left.fsaverage164.label.gii > fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii > lh.HCP-MMP1.annot > > and I get a lot of errors like 'Invalid argument > freadFloat: fread failed > Invalid argument > mrisFindNeighbors: ../../../cortical/fs_L-to-fs_ > LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii.1: face[1].v[0] = 0, > but face 1 not in vertex 0 face list > > Invalid argument > Segmentation fault (core dumped)' in the shell. > > Any suggestions? > > Thanks again > > > > *Francesco Sammartino MD* > > On Wed, Oct 12, 2016 at 11:18 AM, Elam, Jennifer wrote: > >> Hi Francesco, >> >> This has been discussed quite a bit on the list. Please see >> https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03000.html >> and other messages on the thread, especially the discussion of the price >> you pay in terms of spatial fidelity when you convert from surface to >> volume. >> >> >> Also see this article “The Human Connectome Project’s neuroimaging >> approach” <http://www.nature.com/neuro/journal/v19/n9/full/nn.4361.html> >> published in Nature Neuroscience in late August 2016 that discusses this >> issue. >> >> >> Note that FSL is currently working on getting CIFTI compatibility in >> their next release, which should be coming out soon. >> >> >> Best, >> >> Jenn >> >> >> Jennifer Elam, Ph.D. >> Scientific Outreach, Human Connectome Project >> Washington University School of Medicine >> Department of Neuroscience, Box 8108 >> 660 South Euclid Avenue >> St. Louis, MO 63110 >> 314-362-9387 >> e...@wustl.edu >> www.humanconnectome.org >> >> ---------- >> *From:* hcp-users-boun...@humanconnectome.org < >> hcp-users-boun...@humanconnectome.org> on behalf of Francesco Sammartino >> >> *Sent:* Wednesday, October 12, 2016 8:59:54 AM >> *To:* hcp-users@humanconnectome.org >> *Subject:* [HCP-Users] Extract 137 RSN networks - Glasser et al. - >> Nature 2016 >> >> Hi >> >> We are aiming to integrate the new high resolution cortical parcellation >> and the 137 resting state networks into our probabilistic tractography (FSL >> based) pipeline. >> >> Could you please tell me how should I convert to nifti labelmaps the >> content of the file Q1-Q6_RelatedParcellation210.i >> ndividual_RSNs_d137_WR_norm_MSMAll_2_d41_WRN_DeDrift.32k_fs_LR.dscalar.nii >> or direct me to a tutorial/howto on how to project those parcellation >> information to a nifti volume? >> >> We are heavily based on FSL and it would be great to convert all the >> files in its format. >> >> Thanks and sorry for the newbie question. >> >> >> Francesco Sammartino >> >> ___ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Extract 137 RSN networks - Glasser et al. - Nature 2016
Thank you a lot. I found a problem in the last step. When I convert files from gii to annot using mris_convert : I run mris_convert --annot left.fsaverage164.label.gii fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii lh.HCP-MMP1.annot and I get a lot of errors like 'Invalid argument freadFloat: fread failed Invalid argument mrisFindNeighbors: ../../../cortical/fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii.1: face[1].v[0] = 0, but face 1 not in vertex 0 face list Invalid argument Segmentation fault (core dumped)' in the shell. Any suggestions? Thanks again *Francesco Sammartino MD* On Wed, Oct 12, 2016 at 11:18 AM, Elam, Jennifer wrote: > Hi Francesco, > > This has been discussed quite a bit on the list. Please see > https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03000.html > and other messages on the thread, especially the discussion of the price > you pay in terms of spatial fidelity when you convert from surface to > volume. > > > Also see this article “The Human Connectome Project’s neuroimaging > approach” <http://www.nature.com/neuro/journal/v19/n9/full/nn.4361.html> > published in Nature Neuroscience in late August 2016 that discusses this > issue. > > > Note that FSL is currently working on getting CIFTI compatibility in their > next release, which should be coming out soon. > > > Best, > > Jenn > > > Jennifer Elam, Ph.D. > Scientific Outreach, Human Connectome Project > Washington University School of Medicine > Department of Neuroscience, Box 8108 > 660 South Euclid Avenue > St. Louis, MO 63110 > 314-362-9387 > e...@wustl.edu > www.humanconnectome.org > > -- > *From:* hcp-users-boun...@humanconnectome.org humanconnectome.org> on behalf of Francesco Sammartino < > francesco.sammartino....@gmail.com> > *Sent:* Wednesday, October 12, 2016 8:59:54 AM > *To:* hcp-users@humanconnectome.org > *Subject:* [HCP-Users] Extract 137 RSN networks - Glasser et al. - Nature > 2016 > > Hi > > We are aiming to integrate the new high resolution cortical parcellation > and the 137 resting state networks into our probabilistic tractography (FSL > based) pipeline. > > Could you please tell me how should I convert to nifti labelmaps the > content of the file Q1-Q6_RelatedParcellation210. > individual_RSNs_d137_WR_norm_MSMAll_2_d41_WRN_DeDrift.32k_fs_LR.dscalar.nii > or direct me to a tutorial/howto on how to project those parcellation > information to a nifti volume? > > We are heavily based on FSL and it would be great to convert all the files > in its format. > > Thanks and sorry for the newbie question. > > > Francesco Sammartino > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Extract 137 RSN networks - Glasser et al. - Nature 2016
Hi Francesco, This has been discussed quite a bit on the list. Please see https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03000.html and other messages on the thread, especially the discussion of the price you pay in terms of spatial fidelity when you convert from surface to volume. Also see this article “The Human Connectome Project’s neuroimaging approach”<http://www.nature.com/neuro/journal/v19/n9/full/nn.4361.html> published in Nature Neuroscience in late August 2016 that discusses this issue. Note that FSL is currently working on getting CIFTI compatibility in their next release, which should be coming out soon. Best, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> From: hcp-users-boun...@humanconnectome.org on behalf of Francesco Sammartino Sent: Wednesday, October 12, 2016 8:59:54 AM To: hcp-users@humanconnectome.org Subject: [HCP-Users] Extract 137 RSN networks - Glasser et al. - Nature 2016 Hi We are aiming to integrate the new high resolution cortical parcellation and the 137 resting state networks into our probabilistic tractography (FSL based) pipeline. Could you please tell me how should I convert to nifti labelmaps the content of the file Q1-Q6_RelatedParcellation210.individual_RSNs_d137_WR_norm_MSMAll_2_d41_WRN_DeDrift.32k_fs_LR.dscalar.nii or direct me to a tutorial/howto on how to project those parcellation information to a nifti volume? We are heavily based on FSL and it would be great to convert all the files in its format. Thanks and sorry for the newbie question. Francesco Sammartino ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Extract 137 RSN networks - Glasser et al. - Nature 2016
Hi We are aiming to integrate the new high resolution cortical parcellation and the 137 resting state networks into our probabilistic tractography (FSL based) pipeline. Could you please tell me how should I convert to nifti labelmaps the content of the file Q1-Q6_RelatedParcellation210.individual_RSNs_d137_WR_norm_MSMAll_2_d41_WRN_DeDrift.32k_fs_LR.dscalar.nii or direct me to a tutorial/howto on how to project those parcellation information to a nifti volume? We are heavily based on FSL and it would be great to convert all the files in its format. Thanks and sorry for the newbie question. Francesco Sammartino ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
