Dear all, Thank you so much! It works now.
Helen
On Mar 1, 2013, at 2:41 PM, Mark Jenkinson wrote:
Hi,
It looks like your installation isn't right - you need FSL5.0 or higher for this to work. If not I would expect it to complain about: "Unrecognised cost function type: bbr" as it seems to do.
Maybe you should check that you are picking up the right version of FSL, by doing: which flirt and echo $FSLDIR
Only if these are both pointing at the same place and are installations of FSL5.0 or higher, would this work.
All the best, Mark
On 1 Mar 2013, at 19:31, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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: 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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Chen, Xiaoyan