[Freesurfer] Using Nifti parcellation with Freesurfer

Dear Freesurfer community, I would like to be able to use any preexisting Nifti atlas with Freesurfer’s parcellation methods. As a proof-of-concept, I am attempting to use the parcellation scheme produced by Finn and colleagues (2015) with mris_ca_train and mris_ca_label. I have some questions

Re: [Freesurfer] Trouble getting git-annex files

PM, Ricardo Valle <ruyval...@gmail.com> wrote: > > Dear Freesurfer community, > > I am trying to recompile Freesurfer in order to get a binary of the latest > version of dmri_train. I have been following the instructions in the > Freesurfer Mac Developer’s page > <h

Re: [Freesurfer] Trouble getting git-annex files

h worked > for me on a Mac, e.g., > after changing mri_train.c, > > $ cd ./freesurfer/mri_train > $ rm -f mri_train mri_train.o > $ make -r mri_train > > - rob > > > > >> On May 2, 2018, at 5:37 PM, Ricardo Valle <ruyval...@gmail.com >> <

Re: [Freesurfer] Trouble getting git-annex files

ich do not get > built just by typing > “make dmri_train” under ./freesurfer/trc when nothing else has been built in > the tre. We can look at trying > to remedy this, but I think the expectation has been that people build from > the top of the tree > (or at least

[Freesurfer] mri_em_register and mri_ca_register

Dear Freesurfer community, I would like to get a better sense of how mri_em_register and mri_ca_register work. I understand the former is a linear registration and the latter is nonlinear, and that they are both meant to register an individual to a template space (MNI152?). Would it be

Re: [Freesurfer] mri_em_register and mri_ca_register

> cheers > Bruce > On Thu, 18 Jan 2018, > Ricardo Valle wrote: > >> Dear Freesurfer community, >> >> I would like to get a better sense of how mri_em_register and >> mri_ca_register work. I understand the former is a linear registration and &g

Re: [Freesurfer] mri_em_register and mri_ca_register

! Ruy > On Jan 18, 2018, at 2:52 PM, Ricardo Valle <ruyval...@gmail.com> wrote: > > I see. Thank you very much! > Cheers, > Ruy >> On Jan 18, 2018, at 1:24 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: >> >> Hi Ruy >> >> they both re

Re: [Freesurfer] mri_em_register and mri_ca_register

correct. The last one (and the follow-on article about > diffusion with Lilla Zollei as first author) is about CVS (combined volume > and surface registration) > > cheers > Bruce > On Wed, 24 Jan 2018, Ricardo Valle wrote: > >> Hi Bruce, >> I would

Re: [Freesurfer] Using subject specific template, atlas, & TPM

Take a look at the bottom of this page: https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > On Feb 6, 2018, at 2:04 PM, Saturne Fox wrote: > > Hey ! > > Is it possible not to receive the mails

[Freesurfer] MRIxfmCRS2XYZtkreg function

Dear Freesurfer community, I have stumbled upon a function called MRIxfmCRS2XYZtkreg in the Freesurfer source code on Github. It is used in several places but does not seem to be defined anywhere in the repository. Is it part of some external library? Would it be possible to take a look at its

Re: [Freesurfer] Problem running mri_convert

Hi Jay, Try calling "source $FREESURFER_HOME/SetUpFreeSurfer.csh” (without the quotes) at the beginning of @SUMA_Make_Spec_FS (it’s a script that should be wherever AFNI is installed, like $HOME/abin). Cheers, Ruy > On Mar 26, 2018, at 12:54 PM, Hoopes, Andrew wrote: