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 <fis...@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-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/
>>>
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>>>
>>>
>>>
>>
>>
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