Re: [Freesurfer] configure overlay display in tksurfer by keyboard inputs
Hi, I have the same problem with tksurfer in Ubuntu. The keyboard entry doesn't work for the tksurfer input boxes - I can't set any values in the overlay configuration window, edit label info, configure phase encoded data display etc. All of the text / numeric entry boxes have this issue. Any suggestions on how to fix this? My freesurfer verion is freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 but I had the same problem before updating to v6-beta. Thanks, David -Message d'origine- De : freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] De la part de Bruce Fischl Envoyé : 15 August 2015 21:12 À : Freesurfer support list Objet : Re: [Freesurfer] configure overlay display in tksurfer by keyboard inputs Hi Lars can you give more details? What prevents you from entering values? Do you get any errors when tksurfer loads? cheers Bruce On Sat, 15 Aug 2015, Lars M. Rimol wrote: > > Hi all, > > I have installed FS 5.3 on an Ubuntu 14.04 system and find that I am > unable to set threshold values in the edit boxes in the "configure > overlay" display in tksurfer. Does anybody know how to fix this (without > specifying the threshold on the command line each time)? > > Thank you! > > > > > > yours, > Lars M. Rimol, PhD > Department of Medicine > John A. Burns School of Medicine > University of Hawai'i > 1356 Lusitana Street, University Tower Honolulu, HI 96813 > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] configure overlay display in tksurfer by keyboard inputs
I use freeview a lot and have never had any problems with it. However I want to work on occipital patches to do retinotopy. Can freeview load flat patches? Is there a way to display complex data overlays to produce phase maps as was possible in tksurfer? Thanks, David -Message d'origine- De : freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] De la part de Bruce Fischl Envoyé : 12 December 2015 16:45 À : Freesurfer support list Objet : Re: [Freesurfer] configure overlay display in tksurfer by keyboard inputs Hi David tksurfer has been deprecated - can you try using freeview instead? Bruce On Sat, 12 Dec 2015, Slater David wrote: > Hi, > > I have the same problem with tksurfer in Ubuntu. > > The keyboard entry doesn't work for the tksurfer input boxes - I can't set > any values in the overlay configuration window, edit label info, configure > phase encoded data display etc. All of the text / numeric entry boxes have > this issue. > > Any suggestions on how to fix this? > > My freesurfer verion is > freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 but I had the same > problem before updating to v6-beta. > > Thanks, > David > > > -Message d'origine- > De : freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] De la part de Bruce > Fischl Envoyé : 15 August 2015 21:12 À : Freesurfer support list Objet > : Re: [Freesurfer] configure overlay display in tksurfer by keyboard > inputs > > Hi Lars > > can you give more details? What prevents you from entering values? Do you get > any errors when tksurfer loads? > > cheers > Bruce > > On Sat, > 15 Aug 2015, Lars M. Rimol wrote: > >> >> Hi all, >> >> I have installed FS 5.3 on an Ubuntu 14.04 system and find that I am >> unable to set threshold values in the edit boxes in the "configure >> overlay" display in tksurfer. Does anybody know how to fix this (without >> specifying the threshold on the command line each time)? >> >> Thank you! >> >> >> >> >> >> yours, >> Lars M. Rimol, PhD >> Department of Medicine >> John A. Burns School of Medicine >> University of Hawai'i >> 1356 Lusitana Street, University Tower Honolulu, HI 96813 >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is addressed. If you believe this e-mail was sent to you in error > and the e-mail contains patient information, please contact the > Partners Compliance HelpLine at http://www.partners.org/complianceline > . If the e-mail was sent to you in error but does not contain patient > information, please contact the sender and properly dispose of the e-mail. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Working with non-FreeSurfer derived meshes and labels
Hi, I have some mesh and label files I would like to use with my Freesurfer data however they are in an alternative format (connectome workbench). I would like to get the labels into the space of a typical Freesurfer subject (e.g. fsaverage), followed by pushing the labels to subject native space and creating volume label files (similar to the aparc native space parcellations). Is it possible to register an isolated mesh file to the fsaverage subject? How can I convert labels on a .gii mesh file to a standard Freesurfer subject? Thanks, David p.s. The goal of this would be to use the following parcellation scheme with my freesurfer data: Gordon, E.M., Laumann, T.O., Adeyemo, B., Huckins, J.F., Kelley, W.M., Petersen, S.E., 2014. Generation and Evaluation of a Cortical Area Parcellation from Resting-State Correlations. Cereb. Cortex bhu239-. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Working with non-FreeSurfer derived meshes and labels
Hi Bruce, I wrote to the HCP user group to ask about this. I received an answer but it’s still unclear to me. As far as I can tell their are tools which can translate Freesurfer surfaces to the HCP/Caret format, but there isn’t a tool to convert in the opposite direction. I simply would like to take a surface parcellation in HCP (32k or 164k) format and resample it to a standard Freesurfer subject (e.g fsaverage). Here is my question and the reply from the HCP user group: Great thanks for your helpful reply. Unfortunately I'm not working with the HCP data exclusively. In addition we have our own data which has been pre-processed with the standard FreeSurfer -recon-all pipeline. Thus these subjects do not have a 32k or 164k mesh, instead they have typical output surfaces from FreeSurfer... So if I understand correctly I could do the following: * Use the '"freesurfer_to_fs_LR" script to create 32k and/or 164k mesh surfaces for each subject * The Gordon parcellation would then have a direct correspondence with these meshes (no resampling required) * The FreeSurfer "mri_label2vol" tool could then be used to create subject specific parcellation maps Is this correct? Am I missing something? Thanks, David -Message d'origine- De : Donna Dierker [mailto:do...@brainvis.wustl.edu] Envoyé : 08 March 2016 18:05 À : Slater David Objet : Re: [HCP-Users] Cortical parcellations in Connectome Workbench and FreeSurfer I hope someone who has actually done something like this answers, but this page might be helpful: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_label2vol I'm less familiar with Freesurfer tools, but conceptually: * The Gordon parcellation is available on 32k mesh (or 164k at least). * The subject's individual surface is available in both of those meshes. * The parcellation could be projected to the ribbon between the white and pial surfaces (possibly via mri_label2vol). * It would not be necessary to resample the parcellation onto the native mesh to do this. * The subject's native mesh is also available in one of the HCP-downloadable packages. * There is a way, using -surface-project-unproject, to convert stuff back to native mesh, but it's tough to get your head around it, and I'm not sure it's the shortest path in this case. Again, hopefully someone who has done this will reply. :) On Mar 8, 2016, at 4:14 AM, Slater David mailto:david.sla...@chuv.ch>> wrote: > Hi, > > I have a parcellation I would like to work with from the following paper: > > Gordon, E.M., Laumann, T.O., Adeyemo, B., Huckins, J.F., Kelley, W.M., > Petersen, S.E., 2014. Generation and Evaluation of a Cortical Area > Parcellation from Resting-State Correlations. Cereb. Cortex bhu239-. > > > The cortical parcellations are saved in .gii format for both the fs_LR 32k > and 164k meshes. My aim is to create a parcellated volume image for each of > my subjects in their native space. I know how to do this with Freesurfer > tools but I am a little lost with the fs_LR 32k and 164k mesh formats. > > If I had the parcellation in a standard Freesurfer subject space (e.g. > fsaverage) I would transform the parcalletion to the subject native space and > convert the surface labels to a volume parcellation. This is similar to how > the aparc niftii files are generated. > > How can I get a parcellation of the fs_LR 32k or 164k meshes into a subject's > native space parcellation? Or alternatively, how can I convert fs_LR 32k or > 164k vertex values to the fsaverage surface? > > Thanks, > David > ___ -Message d'origine- De : freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] De la part de Bruce Fischl Envoyé : 08 March 2016 14:32 À : Freesurfer support list Objet : Re: [Freesurfer] Working with non-FreeSurfer derived meshes and labels Hi David I'm pretty sure that the Wash U HCP group has sorted this out. Have you asked them? cheers Bruce On Tue, 8 Mar 2016, Slater David wrote: > > Hi, > > > > I have some mesh and label files I would like to use with my > Freesurfer data however they are in an alternative format (connectome > workbench). > > > > I would like to get the labels into the space of a typical Freesurfer > subject (e.g. fsaverage), followed by pushing the labels to subject > native space and creating volume label files (similar to the aparc > native space parcellations). > > > > Is it possible to register an isolated mesh file to the fsaverage subject? > How can I convert labels on a .gii mesh file to a standard Freesurfer >
