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
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
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
Hi Helen
it's not called bbr, it's called bbregister.
cheers Bruce On Fri, 1 Mar 2013, 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Chen, Xiaoyan -
Douglas N Greve