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: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, March 01, 2013 2:22 PM
To: freesurfer@nmr.mgh.harvard.edu
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
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
