Hi Helen, that is probably their implementation of BBR, so you should
contact them directly.
doug
On 03/01/2013 02:28 PM, 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/
>
> _______________________________________________
> Freesurfer mailing list
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> 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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