The -cifti-convert command is not the correct command to map volume-based data onto surfaces, its purpose is to take existing cifti data and convert it to formats that can be used to a limited extent in utilities that don't read cifti files (for instance, making what we have referred to as "fake nifti" files).
The central command needed to do what you want is -volume-to-surface-mapping, but you need to have generated individual subject surfaces and ensured they are properly aligned to your volume files before you can use it for its intended purpose. Tim On Wed, Mar 28, 2018 at 3:56 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > I think you might need to contact the Petersen lab for support for their > code. If you have T1w, T2w, field map and fMRI you could use the HCP > Pipelines to get CIFTI timeseries. If you don’t, you might be able to use > CIFTIFY, a beta tool for mapping legacy fMRI data to CIFTI by Erin Dickie: > > https://edickie.github.io/ciftify > > Peace, > > Matt. > > From: Boukhdhir Amal <boukhdhira...@yahoo.fr> > Reply-To: Boukhdhir Amal <boukhdhira...@yahoo.fr> > Date: Wednesday, March 28, 2018 at 3:51 PM > To: Matt Glasser <glass...@wustl.edu> > Subject: Re: [HCP-Users] Conversion from 4D data to Cifti (.dtseries.nii) > > Hello, > > I have preprocessed volume data (4D Nifti) from the CoRR HNU data and I > want to convert these volumes into surface data > to be able to run a Matlab-based parcellation algorithm from Gordon et al, > 2016 (Resources <http://www.nil.wustl.edu/labs/petersen/Resources.html>) > which is based on Cifti time series. > > Resources > > <http://www.nil.wustl.edu/labs/petersen/Resources.html> > > Your help is truly appreciated ! Thank you ! > > > > > Cordialement, > > *Amal Boukhdhir, étudiante Doctorat* > Centre de recherche de l’Institut Universitaire de gériatrie de Montréal > (SIMEXP > lab <http://www.simexp-lab.org/>) > CIUSSS du Centre-Est-de-l’Île-de-Montréal > Bureau M6808 > 4565, Chemin Queen-Mary > <https://maps.google.com/?q=4565,+Chemin+Queen-Mary+%0D%0AMontr%C3%A9al+(Qu%C3%A9bec)+%0D%0AH3W+1W5&entry=gmail&source=g> > Montréal (Québec) > H3W 1W5 > > Département d'informatique et de Recherche opérationnelle (Computer > Vision & Geometric Modeling Lab <http://www.iro.umontreal.ca/%7Elabimage/> > ) > Université de Montréal > CP 6128 Succ centre-ville > Montréal (Québec) > H3C 3J7 > <http://www.iro.umontreal.ca/%7Elabimage/> > > > > Le mercredi 28 mars 2018 à 12:16:53 UTC-4, Glasser, Matthew < > glass...@wustl.edu> a écrit : > > > I would need to know more about your study to best assist you. > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Boukhdhir Amal > <boukhdhira...@yahoo.fr> > Reply-To: Boukhdhir Amal <boukhdhira...@yahoo.fr> > Date: Wednesday, March 28, 2018 at 11:07 AM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] Conversion from 4D data to Cifti (.dtseries.nii) > > Hello, > > I am trying to convert a nifti 4D volume to cifti format but this command > does not provide a useful image: > *./wb_command -cifti-convert -to-nifti path_to_cifti path_to_nifti* > > Is it possible to have a CIFTI version inclusing cortical and subcortical > areas ? Any insights related to that please ? > > > > > Best Regards, > > *Amal Boukhdhir, étudiante Doctorat* > Centre de recherche de l’Institut Universitaire de gériatrie de Montréal > (SIMEXP > lab <http://www.simexp-lab.org/>) > CIUSSS du Centre-Est-de-l’Île-de-Montréal > Bureau M6808 > 4565, Chemin Queen-Mary > <https://maps.google.com/?q=4565,+Chemin+Queen-Mary+%0D%0AMontr%C3%A9al+(Qu%C3%A9bec)+%0D%0AH3W+1W5&entry=gmail&source=g> > Montréal (Québec) > H3W 1W5 > > Département d'informatique et de Recherche opérationnelle (Computer > Vision & Geometric Modeling Lab <http://www.iro.umontreal.ca/%7Elabimage/> > ) > Université de Montréal > CP 6128 Succ centre-ville > Montréal (Québec) > H3C 3J7 > > > > > Cordialement, > > *Amal Boukhdhir, étudiante Doctorat* > Centre de recherche de l’Institut Universitaire de gériatrie de Montréal > (SIMEXP > lab <http://www.simexp-lab.org/>) > CIUSSS du Centre-Est-de-l’Île-de-Montréal > Bureau M6808 > 4565, Chemin Queen-Mary > <https://maps.google.com/?q=4565,+Chemin+Queen-Mary+%0D%0AMontr%C3%A9al+(Qu%C3%A9bec)+%0D%0AH3W+1W5&entry=gmail&source=g> > Montréal (Québec) > H3W 1W5 > > Département d'informatique et de Recherche opérationnelle (Computer > Vision & Geometric Modeling Lab <http://www.iro.umontreal.ca/%7Elabimage/> > ) > Université de Montréal > CP 6128 Succ centre-ville > Montréal (Québec) > H3C 3J7 > <http://www.iro.umontreal.ca/%7Elabimage/> > > _______________________________________________ > 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
