Hi Mark,
This is indeed an issue in fugue with regard to reading the input mask
image - it assumes that there is a single connected background
component, which is not the case in your data. We will get it fixed
for the next FSL release.
Cheers,
Paul
On 03/04/2019, Mark Wagshul <[log in to unmask]> wrote:
> 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]
>
>
> This email message and any accompanying attachments may contain privileged
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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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