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Hi, FSL doesn’t generally like it when there are two files with the same basename but different extensions. Try using a totally different name. If that still fails try: fslmaths original_name new_name And then try bet on the new_name version. It is possible that some fields in the file are not set to correct NIFTI settings and hence some tools complain. Running it through fslmaths like this can fix that in certain circumstances. If this also fails then see if fslhd will give you any useful output. All the best, Mark On 4 Jun 2019, at 20:46, Banik, Rana <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hey Mark, It was a gunzipped file then I unzipped it using Matlab and both files works pretty well in both Python(nibabel) and Matlab. Now as you have said I tried with .nii.gz extension which ends up the same. <image001.png> Rana Banik Graduate Student Dept. of Biomedical Engineering<https://engineering.vanderbilt.edu/bme/> Vanderbilt University<https://www.vanderbilt.edu/> Contact: +16152756216<x-msg://737/+16152756216> From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> On Behalf Of Mark Jenkinson Sent: Tuesday, June 4, 2019 2:37 PM To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [FSL] regarding FSL in windows Hi, I’m not really sure what is going on here but some random things that might be worth trying, based on some past experiences on the list are: - Is it in fact a gzipped file that is misnamed? Try renaming it with the extension .nii.gz and see if that fixes it. - Are the weird non-standard characters in the filename? Try completely changing the name and see if that helps. - Do ‘ls -la’ in the directory and see if it is zero length or something odd (e.g. no read permission, broken alias, etc.) - Try reading it into python or matlab or with some other tool, to see if it is an FSL problem or a problem with the file itself. All the best, Mark On 4 Jun 2019, at 20:10, Banik, Rana <[log in to unmask]<mailto:[log in to unmask]>> wrote: The same things going on… Is there any syntax or file format/extension that I need to be aware of? <image001.jpg> Rana Banik Graduate Student Dept. of Biomedical Engineering<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fengineering.vanderbilt.edu%2Fbme%2F&data=02%7C01%7Crana.banik%40VANDERBILT.EDU%7C6b1fd4f9c4ae4ab7f9d408d6e924173d%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636952738558555621&sdata=CLm5GxcBYVx3febNrOCnwefnx%2Fi4e1VAcsgLuC48%2FIk%3D&reserved=0> Vanderbilt University<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.vanderbilt.edu%2F&data=02%7C01%7Crana.banik%40VANDERBILT.EDU%7C6b1fd4f9c4ae4ab7f9d408d6e924173d%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636952738558565622&sdata=JUj2BfvVkcDOOoXh8LVRLopa1hVR6nvPiVRmP7gw7kI%3D&reserved=0> Contact: +16152756216<x-msg://734/+16152756216> From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> On Behalf Of Braimah, Adebayo (Adebayo) Sent: Tuesday, June 4, 2019 1:55 PM To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [FSL] regarding FSL in windows I am not exactly too sure of the behavior of the GUI in this case. Try navigating to that directory and typing: `bet <input_image> <output_image> -m` -- Thank You for Your Time Adebayo Braimah Research Assistant III Pediatric Neuroimaging Research Consortium Imaging Research Center Cincinnati Children's 3333 Burnet Avenue, MLC 5033 Cincinnati, OH 45229 E-mail: [log in to unmask]<mailto:[log in to unmask]> Phone: +1 (513) 636-3946 https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DFSL%26A%3D1&data=02%7C01%7Crana.banik%40VANDERBILT.EDU%7C6b1fd4f9c4ae4ab7f9d408d6e924173d%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636952738558565622&sdata=pF1bQx79v7kVajNuNYj0NHPRXCp8s6tqilRZNT39y74%3D&reserved=0> ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DFSL%26A%3D1&data=02%7C01%7Crana.banik%40VANDERBILT.EDU%7C6b1fd4f9c4ae4ab7f9d408d6e924173d%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636952738558575609&sdata=C4Y5J%2BevanlYKQ1hQLIgEfFUE%2FQFJ95%2FKPxaIxVZIgw%3D&reserved=0> ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DFSL%26A%3D1&data=02%7C01%7Crana.banik%40VANDERBILT.EDU%7C6b1fd4f9c4ae4ab7f9d408d6e924173d%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636952738558575609&sdata=C4Y5J%2BevanlYKQ1hQLIgEfFUE%2FQFJ95%2FKPxaIxVZIgw%3D&reserved=0> ________________________________ 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