[Freesurfer] Skipping time consuming FS parts.

Dear FS experts, I have a large data set which I want to recon-all, in order to obtain the cortical, sub-cortical parcellations and the corresponding volumes and thicknesses. As the reconstruction is very time-consuming I was wondering which steps I might skip without significant decrease in

Re: [Freesurfer] Skipping time consuming FS parts.

Hi Mohammed, sorry, you can't really skip any of it if you want those results. cheers, Bruce On Fri, 26 Mar 2010, Mohammed el Morabit wrote: > > > Dear FS experts, > > I have a large data set which I want to recon-all, in order to obtain the > cortical, sub-cortical parcellations and the corr

[Freesurfer] Poor Talairach registration and effect on ICV

Hi, in our population of MCI patients, unfortunately parts of the cerebellum were not completely scanned. I ran the data throught the whole FS-4.5.0 pipeline and I see that the eTIV normalized volumes of the segmented structues have very large variance compared to the eTIV normalized group of i

Re: [Freesurfer] Poor Talairach registration and effect on ICV

Hi Martin, I guess that might work. It's hard for us to speculate as we've never tried anything like it Bruce On Fri, 26 Mar 2010, Martin Kavec wrote: > Hi, > > in our population of MCI patients, unfortunately parts of the cerebellum were > not completely scanned. I ran the data throught the who

Re: [Freesurfer] changing watershed threshold has no effect

Something like that I would say you usually have to manually edit. Allison -- On Fri, 26 Mar 2010, Andreas Berger wrote: > hello freesurfers, > > we are having a problem with insufficient skull stripping, in 66 out > of 200 subjects this affects the pial surface, as can be seen in the > attache

Re: [Freesurfer] Poor Talairach registration and effect on ICV

Thanks a lot for the opinion, Bruce! >From practical point of view, removing the cerebellum from each subjuct should be rather easy since I have its segmentation. Howabout the template? Is there any segmentation of the cerebellum for the template, or I would have to do it manually? I suppose I

Re: [Freesurfer] Freesurfer Digest, Vol 73, Issue 64

Hi Andreas: As far as I know, the complete command is: recon-all -s subjid -skullstrip -no-wsgcaatlas -wsthresh 35 -clean-bm Sincerely, Gonzalo Rojas Costa Laboratory of Medical Imaging Processing Department of Radiology Clínica Las Condes Santiago Chile > Date: Fri, 26 Mar 2010 11:07:0

[Freesurfer] calculate the average thickness of a ROI around PCC

Hi, there, I'd like to measure the average thickness of a ROI around PCC (posterior cingulate cortex). I only have its MNI152 coordinate (-2, -45, 34). How can I calculate its corresponding RAS and Talaraich coordinate, is there an equation? Thanks! Guang