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Thank you Mahmoud, I was using BET gui for that and after tried viewing using fsleyes i figured out the problem. It was because the shared folder was not mounted successfully and thus all the nifti files were empty after transfer. After i got them transfer properly, i am able to extract the brain now. Mystery solved. Thank you for the tip! best, Mark ________________________________ From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Mahmoud <[log in to unmask]> Sent: Monday, January 14, 2019 1:57:38 PM To: [log in to unmask] Subject: Re: [FSL] Brain Extraction using BET on ADNI dataset Hi Mark, Can you share the command that you used? Are you able to open that image in Fsleyes? Mahmoud On Mon, Jan 14, 2019 at 1:33 PM Ke Xu <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi all, thank you for reading this message. I recently started a research and obtained some structural MRI from ADNI1 dataset. When trying to perform brain extraction using BET in FSL, it came up with following error: Image Exception : #22 :: Failed to read volume /home/fsluser/Desktop/subject1 Error : Error: short read, file may be truncated Does anyone have some experience in processing ADNI dataset or have some clue on this matter? thanks, Mark ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1