It is giving you values for two segmentations: inside the label and outside the label. Use --id 1 to get only values inside the cortex label
On 9/9/2020 11:27 AM, vittal korann wrote:
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Dear FreeSurfer experts
I am working on the gyrification index of schizophrenia patients. I had collated global brain values such as thickness, GM, and WM volumes. In addition, I wanted to tabulate gyrification values. Using the below link I was able to extract the hemispheric mean gyrification values. https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31829.html
But it is giving me 2 rows of output that are adding more ambiguity to the existing problem. Below is the command which I used to get mean gyrification for the left hemisphere and also the corresponding output.
*Command Line: * mri_segstats --slabel CSRI104 lh /usr/local/freesurfer//subjects/CSRI104/label/lh.cortex --i /usr/local/freesurfer//subjects/CSRI104/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats *Output: * # NRows 2 # NTableCols 10 # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 6879 4687.8 Seg0000 2.4509 0.2838 1.8067 2.8873 1.0806 2 1 128054 84259.7 Seg0001 3.0148 0.6366 1.9369 4.7611 2.8242My confusion is that which row I should take it as a mean gyrification value for the left hemisphere (seg0000 or seg0001)?
Please guide me if there is a way to combine two hemispheric values and make it as mean gyrification alike mean thickness.
With regards Korann
On Wed, Sep 9, 2020 at 4:51 PM vittal korann <vittalkorann@gmail.com mailto:vittalkorann@gmail.com> wrote:
FreeSurfer experts I am trying to extract the mean gyrification values for the whole brain alike cortical thickness. We have all the whole-brain parameters in 'aparc.stats' file. But we do not have one for the gyrification index. Is there a way to do it? Would be grateful for your help. Best Korann */ /*
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