Re: [Freesurfer] Extracting LGI values

Hi Alan,

lGI is different from the folding index. lGI is not yet extracted automatically in the different regions, because it's more meant to be use at the vertexwise level. But you can easily obtain the lGI values averaged over the Desikan's ROI using the following command:

mris_anatomical_stats -a SUBJ/label/?h.aparc.annot -t SUBJ/surf/?h.pial_lgi -f SUBJ/stats/lh.aparc_lgi.stats SUBJ ?h

Please note than then you will get the average lGI values for each region for each subject under the thickness column, and that the volume in this same text file will not mean anything relevant anymore.

Then you can go for:

aparcstats2table --subjects ALL_YOUR_SUBJECTS --hemi ?h --meas thickness --parc aparc_lgi --tablefile aparc_lgi_?h.txt

Let me know if you have difficulties,

Marie

On Sep 3, 2013, at 1:53 PM, Alan Francis alandarkenergy@gmail.com wrote:

Hi Marie et al,

I have run recon all on the data and calculated LGI for all the brains in my dataset. How does one go about extracting LGI values for each region (eg left Pars Triangularis). Is the Folding index given in the aparc stats sheet the same as LGI?

thanks so much,

Alan