Dear Freesurfer Experts, I would like the mean surface area measures of each cluster i found using command line (mri_glmfit). I used mri_glmfit for a group comparison in surface area between a patient group and a healthy control group. I found 4 different significant clusters (using FDR corrected, is not Clusterwise Correction for Multiple Comparisons). I would like to extract the mean surface area of each significant cluster in the patient group and in the healthy control group. Where can i found the file with this information? thanks!
Bo Xiang
There is not a file with this information; you have to create it. When you run mri_glmfit, you supplied an input file (sometimes called y.mgh). Assuming that this has the surface area in it, then then the y.mgh is all the data for all the subjects in the fsaverage space. Using tksurfer or freeview, create a label file for each of you clusters. You can then use mri_segstats, something like
mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label --avgwf avg.dat --id 1
avg.dat will have one column and number of rows equal to the number of subjects
doug
On 01/24/2013 09:06 PM, xiangbo_2010 wrote:
Dear Freesurfer Experts, I would like the mean surface area measures of each cluster i found using command line (mri_glmfit). I used mri_glmfit for a group comparison in surface area between a patient group and a healthy control group. I found 4 different significant clusters (using FDR corrected, is not Clusterwise Correction for Multiple Comparisons). I would like to extract the mean surface area of each significant cluster in the patient group and in the healthy control group. Where can i found the file with this information? thanks! Bo Xiang
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Douglas N Greve -
xiangbo_2010