Re: [Freesurfer] fornix segmentation using recon-all

2016-07-10 Thread Hari Guragain
Dear Bruce, When I used the mri_cc command and used the -f and -force options, I could see the fornix.mgz file. I wonder how can I get the volume in mm^3 of the structure "fornix" from the above file? I couldn't see the volume of fornix in the aseg.stat file. It would be great if I could find the

Re: [Freesurfer] Regarding: Concatenating hippocampal to generate sig.mgh

2016-07-10 Thread Bruce Fischl
Hi Sampada can you elaborate a bit? What are you trying to achieve? Do you want an average hippocampus? Average maps of subfields? What hypothesis are you trying to test? The individual subject data is not resampled to a common coordinate system, so just averaging them as is won't produce anyth

Re: [Freesurfer] Question about write_surf.m

2016-07-10 Thread Bruce Fischl
no, the extension should be fine. Can you include the entire correspondence in your email as well as the command and the output of it? thanks Bruce On Sat, 9 Jul 2016, Dulce Maria Magdaleno Arroyo wrote: Thank you for replied me!  :) Oh, sorry! but even If a remove the back slash in the fil

Re: [Freesurfer] TRACULA tract group comparison p-values

2016-07-10 Thread Barbara Kreilkamp
Dear Anastasia, Thank you, yes that was exactly what I was attempting to do. Would you be able to assist me with this following question as well please? How would I be able to use a different colormap under point sets please? I can only find "solid color" and "heatmap" but for example a blue-y