[Freesurfer] manual entry for mri_concat

Dear FS experts, I recognized that there is no manual entry for mri_concat and fslcalc.fsl. Although there is an extensive help text just typing the command I would find a manual entry (man mri_concat) including exmaples very helpful (or an entry on the freesurfer command site). Thanks, Michae

[Freesurfer] R: How means all the output file from a segmentation?

Hi Bruce, Thanks for your attention, Can you write for me a sample line where I want to compute a 3D volume of the hippocampal? And I can show it with tksurfer? Thanks Leonardo -Messaggio originale- Da: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Inviato: sabato 12 giugno 2010 20.22

Re: [Freesurfer] Processing need more time using freesurfer

was it the same subject? If not, check for large topological defects, which are usually the most time consuming part cheers Bruce On Sun, 13 Jun 2010, Zhangyuanchao wrote: Hi, expert,   I used freesurfer on a 32bit ubuntu operation system some days ago. For one subject, the "recon-all -s $f

Re: [Freesurfer] R: How means all the output file from a segmentation?

Hi Leonardo, you just want to visualize it? Can you explain your goals a bit better? You could view it in freeview as an isosurface if you wanted. Ruopeng: is there wiki documentation for this? cheers Bruce On Sun, 13 Jun 2010, Leonardo Chesi wrote: > > Hi Bruce, Thanks for your attention,

[Freesurfer] Depth of sulci from ?h.sulc

I located some discussions but could noit figure out how can I obtain numerical depth values from ?h.sulc files. I need to find the sulcal dept of certain sulci as defined in aparc.a2009 Thanks in advance Lena This message has been checked for viruses but the contents of an attachment may still c

[Freesurfer] R: R: How means all the output file from a segmentation?

Hi bruce, my goal is to obtain a 3D surface of the hippocampal region for a visual comparison with a manual segmentation made by a neuroradiologist. Today I managed to extract the volume with mri_binarize but I can't transform it in a surface that tkurfer can visualize. For that I try to use mri_vo

Re: [Freesurfer] standard deviation map

Hi Michael, sorry, a bunch of us have been away in Barcelona with very slow network access. Did this question get answered? I think Doug has something to do this (as do I somewhere, but I'm sure Duog's is better :>) cheers Bruce On Mon, 7 Jun 2010, Michael Scheel wrote: > Dear FS experts, >

Re: [Freesurfer] Depth of sulci from ?h.sulc

Hi Lena, the values in sulc are the integrated dot product of the movement vector with the surface normal, although at the end the global mean is taken out of it. Will that work for you? cheers Bruce On Sun, 13 Jun 2010, Lena Palaniyappan wrote: > I located some discussions but could noit fi

Re: [Freesurfer] R: R: How means all the output file from a segmentation?

vol2surf won't work - that's for scalar maps. You need a tesselation I guess, which you can generate with mri_tesselate or mri_mc. If it's just for visualization though you could probably just load it into freeview and look at it as an isosurface of the volume. cheers Bruce On Sun, 13 Jun 2010,

Re: [Freesurfer] Depth of sulci from ?h.sulc

That should as I am only trying to look at the rank order across two groups in terms of the 'depth'. How can I obtain these numerical values? Thanks Lena On 13/06/2010 19:28, "Bruce Fischl" wrote: > Hi Lena, > > the values in sulc are the integrated dot product of the movement vector > with t

Re: [Freesurfer] Depth of sulci from ?h.sulc

Hi Lena, just use it as you would thickness. Not sure I understand your question. Are you using qdec? cheers Bruce On Sun, 13 Jun 2010, Lena Palaniyappan wrote: > > That should as I am only trying to look at the rank order across two groups > in terms of the 'depth'. How can I obtain these nume