Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

Yes! I got better results now! Thanks!! On Thu, Feb 22, 2018 at 12:57 AM Kirstie Whitaker wrote: > Hi Foucalt, > > I think you need to set the threshold to slightly larger than 0 otherwise > you're taking the center of mass of the whole image (including the 0s) when > really

Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

Hi Foucalt, I think you need to set the threshold to slightly larger than 0 otherwise you're taking the center of mass of the whole image (including the 0s) when really you want to exclude the 0s and only look at the individual regions. I changed --thmin 0 to --thmin 0.1 and the results looked

Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

Attach name file and result file. Thank you for your time! Best, Foucault On Wed, Feb 21, 2018 at 5:24 PM, zuxfoucault Wong wrote: > Hi Kirstie, > > Thank you very much for the suggestions! > I modified my snippet to prevent it from looping the same value and still >

Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

Hi Kirstie, Thank you very much for the suggestions! I modified my snippet to prevent it from looping the same value and still got the same results? ## input=($(cat ./names_68parc.txt)) labels=() hemis=() j=0 for i in "${input[@]}"; do if [[ $i == lh_* ]]; then hemis[j]="lh" i=$(echo $i |

Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

Hi Foucault, In the snippet you added you don’t define the labels variable (which you subsequently loop over in for label in ${labels}). There are two possible mistakes that are easy to fix. One may be that you forgot to read in the labels! And the other is that to get all the values in an

[Freesurfer] Extracting the centroids from Desikan-Killiany atlas

Dear Freesurfer experts, Based on this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/07.html , I wrote a short script to extract the centroids from Desikan-Killiany atlas. ## for hemi in lh rh; do mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir