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Hi everyone,

I'm working on a dataset where T1 scans were taken before the patients went under surgery. During the procedure, a small, non-pathological brain tissue sample was resected from the temporal cortex. The sample, extracted 4cm from the anterior pole within the middle temporal gyrus (Brodmann area 21), measured 1-1.5 cm in diameter. My goal is to extract the MRI-derived cortical thickness from that tissue on the T1 scan. My first step was creating a sphere as my ROI with the coordinates that I decided by participants (through looking at fsleyes). The problem now is that I'm unsure on how to extract the cortical thickness from that ROI for each participant. Do I need to register my ROI into the inflated template? If you have any ideas or codes to solve that issue, please let me know.

Here the script that I used to get the sphere: # choose radius radius=20 # in mm

# replace with image of your subject subj_image='/Project_2.5/MRI/Subject_103/Scan103.nii.gz'

# NB, these are not MNI coordinates, but coordinates in the so called voxel space # change to the coordinates you are interested in coordinate_x=70 coordinate_y=53 coordinate_z=32

## do not change anything below fslmaths ${subj_image} -mul 0 -add 1 -roi ${coordinate_x} 1 ${coordinate_y} 1 ${coordinate_z} 1 0 1 _tmp_point -odt float fslmaths _tmp_point -kernel sphere ${radius} -fmean spherical_roi_r${radius} -odt float rm -f _tmp_point.nii.gz

fsleyes ${subj_image} spherical_roi_r${radius}.nii.gz &

Thank you for your help, Lea

__________________________________________________________ Léa C. Michel PhD Student Lifespan Cognitive Dynamics Lab - www.rogierkievit.comhttp://www.rogierkievit.com/ Affiliation: Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Cognitive Neuroscience Department, Nijmegen, The Netherlands Email: Lea.Michel@radboudumc.nl Website: https://leacmichel.github.io/ Twitter: @LeaCMichelhttps://twitter.com/LeaCMichel

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