great! thank you so much Angela
Sorry, the input should be area, not thickness, ie,
mri_segstats --i $SUBJECTS_DIR/fsaverage/lh.white.avg.area.mgh --seg gyrbin.mgh --id 1 --sum gyrbin.sum
On 11/2/14 11:30 AM, Douglas Greve wrote:
First, create binary masks, something like (for a threshold of 2 = p < .01)
mri_binarize --i gyrification/sig.mgh --abs --min 2 --binval 1 --o gyrbin.mgh mri_binarize --i thickness/sig.mgh --abs --min 2 --binval 2 --o thickbin.mgh fscalc gyrbin.mgh mul thickbin.mgh mul 3 -o gyr_and_thick_bin.mgh
To get the areas of each, run mri_segstats --i $SUBJECTS_DIR/fsaverage/lh.avg_thickness --seg gyrbin.mgh --id 1 --sum gyrbin.sum mri_segstats --i $SUBJECTS_DIR/fsaverage/lh.avg_thickness --seg thickbin.mgh --id 2 --sum thickbin.sum mri_segstats --i $SUBJECTS_DIR/fsaverage/lh.avg_thickness --seg gyrbin.mgh --id 3 --sum gyr_and_thick_bin.sum
To get maps you can view, fscalc gyrbin.mgh sum thickbin.mgh -o gyr_sum_thick_bin.mgh This creates a map where 1=gyr, 2=thick, and 3=both Run mris_seg2annot on this map to create an annotation which you can then load onto a surface
doug
On 11/2/14 10:58 AM, angela.favaro@unipd.it wrote:
Thank you Bruce!
I have another question: I would like to show the statistical maps of differences in gyrification and those of cortical thickness. Is it possible with freeview? I would also like to calculate the degree of overlapping between these two maps (percentage of vertices or mm2). Is it possible?
thank you!
Angela
Hi Angela
in tksurfer you can show the overlay, and use the "custom fill" button to fill the area that is above threshold on the surface. Then save it as a label and use mri_label2vol to write it into a volume. If the output volume you give has the extension .nii.gz it will save it in nifti for you
cheers Bruce
On Sun, 2 Nov 2014, angela.favaro@unipd.it wrote:
Dear all, I found some interesting findings about gyrification and I would like to test any related problem in structural connectivity. My idea was to use the area where I found significant lower gyrification in my sample to perform probabilistic tracking with FSL. My question is: is there any way to label the area of significant difference (or I have to manually draw it) and to transform it in a nifti format?
Angela
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