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: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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
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