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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
Affiliation: Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Cognitive Neuroscience Department, Nijmegen, The Netherlands
Email: Lea.Michel@radboudumc.nl
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