Re: [Freesurfer] Trouble getting git-annex files

2018-05-03 Thread Ricardo Valle
t; “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 do that once). > > - rob > > >> On Ma

Re: [Freesurfer] Trouble getting git-annex files

2018-05-02 Thread Ricardo Valle
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 > <mailto:ruyval...@gmail.com>> wrote: >> >>

Re: [Freesurfer] Trouble getting git-annex files

2018-05-02 Thread Ricardo Valle
PM, Ricardo Valle 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 > <https://surfer

[Freesurfer] MRIxfmCRS2XYZtkreg function

2018-04-04 Thread Ricardo Valle
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

2018-03-26 Thread Ricardo Valle
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: > > Hi Jay, as a temporar

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

2018-02-06 Thread Ricardo Valle
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 anymore ? > > Best regar

Re: [Freesurfer] mri_em_register and mri_ca_register

2018-01-24 Thread Ricardo Valle
n 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 like to confirm the relationship between a few pape

Re: [Freesurfer] mri_em_register and mri_ca_register

2018-01-24 Thread Ricardo Valle
! Ruy > On Jan 18, 2018, at 2:52 PM, Ricardo Valle wrote: > > I see. Thank you very much! > Cheers, > Ruy >> On Jan 18, 2018, at 1:24 PM, Bruce Fischl wrote: >> >> Hi Ruy >> >> they both register to a .gca atlas that is quite a bit more accurate th

Re: [Freesurfer] mri_em_register and mri_ca_register

2018-01-18 Thread Ricardo Valle
I see. Thank you very much! Cheers, Ruy > On Jan 18, 2018, at 1:24 PM, Bruce Fischl wrote: > > Hi Ruy > > they both register to a .gca atlas that is quite a bit more accurate than > the MNI. The details are in the 2002 and 2004 papers. > > cheers > Bruce > O

[Freesurfer] mri_em_register and mri_ca_register

2018-01-18 Thread Ricardo Valle
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 possib

[Freesurfer] Using Nifti parcellation with Freesurfer

2017-12-08 Thread Ricardo Valle
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