Re: [Freesurfer] LGI for the lobar annotation

The "intensity" is the mean value of the input (lh.pial_lgi in this case) averaged over vertices. If  you wan the total number, multiply it by the number of vertices or re-run with --accumulate. The area is the surface area of the entire lobe. On 4/18/18 3:23 PM, Fernanda Hansen P. de Moraes

Re: [Freesurfer] LGI for the lobar annotation

Sorry, my mistake. mri_segstats --annot DA011 lh lobesStrict --i DA011/surf/lh.pial_lgi --sum lh.lobesStrict.annot.pial_lgi.stats On Wed, Apr 18, 2018 at 4:13 PM Douglas N. Greve wrote: > What is your command line? Also, please remember to post to the list > > > On 04/18/2018 02:10 PM, Fernanda

Re: [Freesurfer] LGI for the lobar annotation

What is your command line? Also, please remember to post to the list On 04/18/2018 02:10 PM, Fernanda Hansen P. de Moraes wrote: > Dear Douglas, > > thank you. > >  The code worked, but I didn't understand the result very well. What > means intensity? The area, is the ara from the piall_lgi surf

Re: [Freesurfer] Recon-all w/ Hammersmith atlas

can you send me Hammers_mith_atlas_n30r83_SPM5.nii.gz  ? On 04/17/2018 07:55 PM, Ryan Flores wrote: > > Hi Doug, > > Thank you for your response. I attempted to run recon-all on the > Hammersmith nifti file as suggested, but unfortunately it appears to > have run into some issues. I’ve attached

Re: [Freesurfer] Lateral Geniculate Nucleus (LGN) roi or volume measures?

Hi Yash we hae some prototypes for LGN but nothing ready for primetime yet sorry Bruce On Mon, 16 Apr 2018, Yash Patel wrote: Hi all,  Is there any way to obtain (automatically, n~1000 subjects), LGN volumes from the Freesurfer set of tools?  Or somehow transform the ROI from an atlas into s

[Freesurfer] HCP Course 2018 at Oxford: Final Course Schedule posted -- Register Now!

Faculty listings and the full schedule of covered topics are now available for the *2018 HCP Course: "Exploring the Human Connectome"

Re: [Freesurfer] How FDR was used to correct for multiple comparisons

Dear Douglas, Thank you for your reply. I read the related FDR paper given in the “mri_fdr –help”. Please tell me if the FDR correction in FreeSurfer do like the below. For the V vertices being tested, the general procedure is as follows: (1) Select a desired FDR bound q between 0 and 1. This i

[Freesurfer] Non-parametric correlation between FC and neuropsychological/volumetric outcomes

Hi list, which the best way to perform a whole-brain correlation of the FC assessed by FS-FAST with the volumetic or neuropsychological outcomes? Please note that my question is specifically addressed to those factors (neuropsycholgical scores or volume of seed) did not show a normal distributio