External Email - Use Caution
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
De informatie in dit bericht is uitsluitend bestemd voor de geadresseerde. Aan dit bericht en de bijlagen kunnen geen rechten worden ontleend. Heeft u deze e-mail onbedoeld ontvangen? Dan verzoeken wij u het te vernietigen en de afzender te informeren. Openbaar maken, kopiëren en verspreiden van deze e-mail of informatie uit deze e-mail is alleen toegestaan met voorafgaande schriftelijke toestemming van de afzender. Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 80262783.
The content of this message is intended solely for the addressee. No rights can be derived from this message or its attachments. If you are not the intended recipient, we kindly request you to delete the message and inform the sender. It is strictly prohibited to disclose, copy or distribute this email or the information inside it, without a written consent from the sender. Radboud university medical center is registered with the Dutch Chamber of Commerce trade register with number 80262783.