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Anderson- Thank you for helping me with this issue. I generated the designs using the fsl/Misc/GLM Setup GUI on a Linux machine. I re-ran but omitted -D, -T and --twopass. This time it passed the crashing point and continued through the 5000 permutations. I did set a typo for output directory when I tested without the flags so nothing wrote out. I'm re-running again to see what the output looks like. As a sanity check, I ran with all flags with the fixed output path and it still crashed, so something about -D, -T and --twopass it doesn't like. -Joel ________________________________ From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Anderson M. Winkler [[log in to unmask]] Sent: Wednesday, February 21, 2018 11:18 PM To: [log in to unmask] Subject: [External] Re: [FSL] Segmentation fault with randomise Hi Joel, How did you generate the design and contrast files? Did you use a Windows computer by any chance...? Also, what happens if you remove options such as -D, -T, and --twopass? All the best, Anderson On 20 February 2018 at 11:54, Bruss, Joel E <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hello- I'm trying to run randomise and keep getting a segmentation fault. It's probably something obvious and apologies if it is. I'm using fsl 5.0.10, Linux. My input file is 256 x 256 x 252 x 41 I created the 4D file in the same order that my mat/con files are in and have verified that the number of entries and number of subs match. For the mat file, NumPoints is listed as 41. My template mask matches the x/y/z dimensions of the input 4D file. My groups and covariates look fine, my contrasts are just G1 > G2, G2 > G1. My randomise command is the following: randomise -i group4D -o twoSampT -d design.mat -t design.con -m groupTemplate_mask.nii.gz -T -D -n 5000 -x --twopass #I've tried this with and without the "-x" option and get the same error. I've run the command in the directory where all of the data lives, I've also tried setting paths, both with the same error. Every time I've run this, it fails at exactly permutation 742. It doesn't matter with machine I use, or which version of fsl (I even tried this on 5.0.2.2). I have a system monitor up and can verify that RAM never goes above ~8 GB (of 16). I've tried searching prior JISCMail threads but I only found two relevant posts, one pointing a time dimension larger than x/y/z and another pointing to a missing flag/argument. It's definitely not the former but possibly the latter? What am I missing in my command or what shouldn't be there? Many thanks in advance. -Joel ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________ ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________