oh, this is the FSL reimplementation of Doug's algorithm (they loved it
so much they had to have their own!). You'll need to ask them about it.
I'll cc MJ so he can chime in.
cheers
Bruce
On Fri, 1 Mar 2013, Chen, Xiaoyan
wrote:
> Doug,
> epi_reg is using BBregister with FSL. In FSL5 they incorporated
> the tool your guys developed. The following is the error message
>
> [mi2b2:OAEAA005] (nmr-stable5.1-env) epi_reg --epi=meanuf-ep2d-18-0001.nii.gz
> --t1=MPRAGE1.nii.gz --t1brain=MPRAGE1_manual2.nii.gz --out=epi2struct.nii.gz
> Running FAST segmentation
> FLIRT pre-alignment
> Running BBR
> Unrecognised cost function type: bbr
> Could not open matrix file epi2struct.mat
> terminate called after throwing an instance of
> 'NEWMAT::IncompatibleDimensionsException'
> /usr/pubsw/packages/fsl/5.0.1/bin/epi_reg: line 353: 47296 Aborted
> (core dumped) $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout}
> --premat=${vout}.mat --interp=spline
> [mi2b2:OAEAA005] (nmr-stable5.1-env) epi_reg --epi=meanuf-ep2d-18-0001.nii.gz
> --t1=MPRAGE1.nii.gz --t1brain=MPRAGE1_manual2.nii.gz --out=epi2struct
> Running FAST segmentation
> FLIRT pre-alignment
> Running BBR
> Unrecognised cost function type: bbr
> Could not open matrix file epi2struct.mat
> terminate called after throwing an instance of
> 'NEWMAT::IncompatibleDimensionsException'
> /usr/pubsw/packages/fsl/5.0.1/bin/epi_reg: line 353: 48263 Aborted
> (core dumped) $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout}
> --premat=${vout}.mat --interp=spline
>
>
>
> Helen
>
> ________________________________________
> From: [email protected]
> [[email protected]] on behalf of Douglas N Greve
> [[email protected]]
> Sent: Friday, March 01, 2013 2:22 PM
> To: [email protected]
> Subject: Re: [Freesurfer] set path for BBR
>
> what is epi_reg? Is that an FS program?
>
> On 03/01/2013 02:19 PM, Chen, Xiaoyan wrote:
>> Hi,
>>
>> If I want to use epi_reg, what do I need to do for the environment in fsl?
>> It says that it's not recognizing the function bbr. How do find the path to
>> BBR in /usr/pubsw?
>>
>> Thank you very much.
>>
>> Helen
>> _______________________________________________
>> Freesurfer mailing list
>> [email protected]
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [email protected]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
> _______________________________________________
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>
>
>
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