Paul,
Thanks for the help. The files have been uploaded, but I have been able to "fix" the problem by using another mask for fugue. I applied a 5 pixel dilation to the T1 brain mask, and fugue runs fine with that. So, it has something to do with the innermask which epi_reg is generating. I don't think it's a mask size issue though, because this mask is only about 1/2 the size of the one produced by epi_reg, and fugue runs in about 8 seconds.
Also, note that the field maps which I am using were produced from my B0 images using fsl_prepare_fieldmap (with the data reconfigured to be consistent with Siemens formatting, I'm on a Philips 3T).
Best,
Mark
____________________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461
Ph: 718-430-4011
FAX: 718-430-3399
Email: [log in to unmask]
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-----Original Message-----
From: FSL - FMRIB's Software Library <[log in to unmask]> On Behalf Of paul mccarthy
Sent: Wednesday, April 3, 2019 2:29 AM
To: [log in to unmask]
Subject: Re: [FSL] Problem with epi_reg
Hi Mark,
Would you be able to:
1. Tell me the OS and version of FSL that you are using
2. Upload the offending data (the inputs to the fugure command-line call) to:
https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Foxfile.ox.ac.uk%2Foxfile%2Fwork%2FextBox%3Fid%3D711708D492B5FAFCF1&data=02%7C01%7Cmark.wagshul%40EINSTEIN.YU.EDU%7C2214dd0c06934f8cb7b508d6b7fdb3b3%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636898697606997240&sdata=twEPuYgJ%2BQyZkx7D3Wi4TKmxkuKbBwh4IFW1q98p0sI%3D&reserved=0
Thanks,
Paul
On 02/04/2019, Mark Wagshul <[log in to unmask]> wrote:
> Dear FSL experts,
>
> I am hoping someone can help me with this problem, either if you've
> seen a similar problem, or know how to better diagnose the problem.
>
> I am attempting to run epi_reg to register my EPI images to my T1's,
> and have run it many times in the past with no problems. So, I'm not
> sure if it is the current subject(s), or something else. I get the
> same behavior on a number of subjects, so it doesn't seem to be a
> specific subject's images which are giving me a problem.
>
> The script runs until the second fugue statement:
>
> /public/apps/fsl/2.0.18/fsl/bin/fugue
> --loadfmap=epi_to_T1_fieldmaprads2str_pad0 --mask=
> epi_to_T1_fieldmaprads2str_innermask --unmaskfmap --unwarpdir=y
> --savefmap= epi_to_T1_fieldmaprads2str_dilated
>
> If I run this fugue command in verbose mode, it appears to be getting
> hung up on the "Regularising the fieldmap" step.
>
> It just sits at this command, with no progress. The one issue which I
> thought might be the problem is the size of the innermask, which is ~
> 4.5M pixels.
>
> Any help would be most appreciated, thanks!
>
> Mark
>
> ____________________
> Mark Wagshul, PhD
> Associate Professor
> Gruss Magnetic Resonance Research Center Albert Einstein College of
> Medicine Bronx, NY 10461
>
> Ph: 718-430-4011
> FAX: 718-430-3399
> Email:
> [log in to unmask]<mailto:[log in to unmask]>
>
> [einstein-logo-rgb]
> This email message and any accompanying attachments may contain
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> strictly prohibited. If you receive this message in error, or are not
> the named recipient(s), please notify the sender at the email address
> above, delete this email from your computer, and destroy any copies in any form immediately.
>
>
>
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