[Freesurfer] Deadline approaching: PhD in visual perceptual learning at the Neural Circuits and Cognition lab @ ENI & German Primate Center Göttingen

2018-10-03 Thread Caspar M. Schwiedrzik
External Email - Use Caution The European Neuroscience Institute in Göttingen (ENI-G) Germany, a partnership between the University Medical Center Göttingen and the Max-Planck-Society, is seeking a *Ph.D. student * About us: The Neural Circuits and Cognition lab of Caspar S

Re: [Freesurfer] Overlay electric field distribution on pial surface

2018-10-03 Thread Meusen - Klooster, D.C.W.
External Email - Use Caution Ah, I see now that my configure screen is clipped, so I can click on all the options but I cannot actually apply them... What are the options for -colortable? If I have those, I can play with the visualization from the command line but I cannot find

Re: [Freesurfer] Overlay electric field distribution on pial surface

2018-10-03 Thread Bruce Fischl
there may be a keyboard shortcut for "apply". Maybe return? Can't you resize the window? On Wed, 3 Oct 2018, Meusen - Klooster, D.C.W. wrote: >External Email - Use Caution > > Ah, I see now that my configure screen is clipped, so I can click on all the > options but I cannot actually ap

[Freesurfer] output values of vertices on surface into a textfile

2018-10-03 Thread Sims, Sara A
External Email - Use Caution Hello! I would like to output the location and value of each vertex on a surface to a text file. How could I go about doing this? Thanks, Sara Sims ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] output values of vertices on surface into a textfile

2018-10-03 Thread Greve, Douglas N.,Ph.D.
mris_convert lh.white lh.white.asc will convert it to ascii. This file will have both xyz coordinates and neighborhood relationships, so you'll have to delete the latter. You can also load the surface into matlab with read_surf.m On 10/03/2018 11:48 AM, Sims, Sara A wrote: > > External

[Freesurfer] hippocampal subfields error

2018-10-03 Thread Marcel Heers
External Email - Use Caution Dear Eugenio, I am currently testing the newest version of your hippocampal subfield analysis script. If I process the data on my macbook the files hipposubfields.lh.T2.v21.file_ID contain the volumes of the different nuclei, but on the linux server th

Re: [Freesurfer] hippocampal subfields error

2018-10-03 Thread Iglesias Gonzalez, Eugenio
External Email - Use Caution That sounds pretty weird… Did you get any error messages on the Linux server? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmic

[Freesurfer] Mac OS free surfer instalation (Vasile, Eduard)

2018-10-03 Thread Vasile, Eduard
academic background and who agreed to be contacted to c.schwiedr...@eni-g.de, preferably before *October 10th, 2018*, but later expressions of interest will be considered until the position is filled. A good command of English is a requirement, but fluency in German is not essential.

Re: [Freesurfer] Mac OS free surfer instalation (Vasile, Eduard)

2018-10-03 Thread Dicamillo, Robert
, and behavioral setups. > > > >ENI-G is engaged in experimental molecular and cellular research on the >central and peripheral nervous systems as well as cognitive and systems >neurosciences research. ENI is pa

[Freesurfer] mri_surf2surf --mapmethod nnf not working?

2018-10-03 Thread Viessmann, Olivia M.
Hello, I am using mri_surf2surf and would like to use the vertex map method nnf ("neighest neighbor, forward only") which according to the --help description exists and avoids multiple source vertices to be mapped and averaged onto a single target vertex (crucial to my analysis here). However,

[Freesurfer] create label from cluster obtained with mri_glm-fit-sim

2018-10-03 Thread Ting Li
External Email - Use Caution Dear Freesurfer Experts, I really need your attention and help. Thanks a lot. We want to create label through the mri_glm-fit-sim cluster results. We have found the same topic in 2013 and tried the method you have provided. However, it doesn’t work

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

2018-10-03 Thread Ting Li
External Email - Use Caution I have also tried the command without annot in specifying the annotation file. Thanks a lot. Regards, Ting > On Oct 3, 2018, at 9:36 PM, Ting Li wrote: > > Dear Freesurfer Experts, > > I really need your attention and help. Thanks a lot. > > We w

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

2018-10-03 Thread Ting Li
External Email - Use Caution Dear Freesurfer Expert, I have figured out the problem is that I didn’t specify lh before the annot file. However, in this method, I didn’t get the right label for I have loaded the label into the subject file. It is the scatter points. I want to c

Re: [Freesurfer] mri_surf2surf --mapmethod nnf not working?

2018-10-03 Thread Greve, Douglas N.,Ph.D.
Are you worried about where it says "Using surf2surf_nnfr()"? There is actually one one function that performs both kinds of mapping. In this case, it is not doing the reverse loop. You can reassure yourself by running it with nnfr and see that it prints out "Surf2Surf: Reverse Loop" (which does