Re: [Freesurfer] Definition of anatomical features

Hi S.V they are all volumes I think. The definitions can be found in various Kennedy/Caviness papers (which we cite in our original 2002 aseg paper in Neuron). cheers Bruce On Fri, 18 May 2018, SJ JV wrote: External Email - Use Caution Hi Can someone please give the

Re: [Freesurfer] gcs and gca to coordinates

Hi Tim the gcs files are on the surface, so it is not so trivial.If you are looking for MNI coords probably the easiest thing to do is use the .annot files that we distribute with fsaverage. For the .gca, you can convert a "frame" of it to a nifti volume via: mri_convert file.gca#0

Re: [Freesurfer] T2 seq. for hippocampus ??

External Email - Use Caution I think it’s an empirical question. I would try both on a bunch of subjects and then decide. But my gut feeling is that T1+T2 will do best. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University

[Freesurfer] Error results mris_make_surfaces

External Email - Use Caution Hello, experts I have a problem with the results of mris_make_surfaces to pial and white matter surfaces. I am working with high resolution (0.75x0.75x0.75) monkey images, mris_makes_surfaces finish without errors but the surfaces have notches, I

[Freesurfer] T2 seq. for hippocampus ??

External Email - Use Caution Hi All, I have 1x1x3 cubic mm T2 and 1x1x1 cubic mm FLAIR, in addition to 1x1x1 cubic mm MPRAGE. Can you please let me know whether I should use only T1 or should I use one of the additional seq. for hippocampal subfield segmentation ? cheers Nik

[Freesurfer] gcs and gca to coordinates

External Email - Use Caution Dear all, thanks for building and maintaining freesurfer. It's really a great tool. My question is very simple: I have three Freesurfer Atlas files (lh and rh curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs and RB_all_2008-03-26.gca) and

Re: [Freesurfer] LGI trouble with Matlab

External Email - Use Caution Hi, probably you need to add MATLAB path to Freesurfer's $PATH variable. The following link may help: http://www.manuelschutze.com/?p=297 On 18 May 2018 at 12:02, subin oh wrote: > External Email - Use Caution > >

[Freesurfer] LGI trouble with Matlab

External Email - Use Caution Hello, I downloaded the Freesurfer ver 5.3.0 and installed it on Mac OS. I run *"recon-all -s -local GI" *for my subject.. And I run *Matlab Script* about "*Start up" , "make_outer_surface", "make_roi_paths" , "find correspoding center" *as follows: