Thanks!
----- Original Message -----
From: "Mark Jenkinson" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Friday, July 10, 2009 9:35 AM
Subject: Re: [FSL] FIRST:fimbria included in the hippocampal volume
> Hi,
>
> I believe that it should be.
> The model used to build FIRST is based on segmentations generated from
> the Center for Morphometric Analysis in Boston, and so it is their
> protocol
> for segmentation that determines what is, or is not, included.
> The relevant document is:
> http://www.cma.mgh.harvard.edu/manuals/segmentation/
> which indicates that the fimbria is included.
> However, you may not get very consistent results for such small
> structures,
> depending on your contrast and resolution.
>
> All the best,
> Mark
>
>
> On 9 Jul 2009, at 18:16, Thomas Doring wrote:
>
>> Dear FSL group,
>> does somebody know if the fimbria is part of the hippocampal volume
>> when using First for segmentation?
>> Thanks for help,
>> Thomas
>> ----- Original Message -----
>> From: Saad Jbabdi
>> To: [log in to unmask]
>> Sent: Thursday, July 09, 2009 1:54 PM
>> Subject: Re: [FSL] bedpostX and tbss_2_reg
>>
>> Hi Xin,
>>
>> See below:
>>
>>>
>>> 1. When I run BedpostX, I get an error at the end that says:
>>> /usr/local/fsl/bin/bedpostx: line 220: 11092 Terminated
>>> ${subjdir}.bedpostX/monitor
>>> However, I seem to be able to trace fibers just fine and they look as
>>> expected. Can someone tell me what this error is about and whether it
>>> affects the results?
>>
>> Don't worry about this error. As long as you can see files such as
>> merged_th1samples in your bedpostx directory, everything should be
>> fine.
>>
>>>
>>> 2. I am trying to edit the tbss_2_reg script to pass on fnirt options
>>> into fsl_reg so that I can include masks in the registration process,
>>> but it didn't work. I basically edited the do_reg function to:
>>>
>>> do_reg(){
>>> f=$1
>>> for g in `$FSLDIR/bin/imglob *_FA.*` ; do
>>> o=${g}_to_$f
>>> mysub=`basename ${g} _FA_FA.nii.gz`
>>> if [ ! -f ${o}_warp.msf ] ; then
>>> echo $o
>>> touch ${o}_warp.msf
>>> echo "$FSLDIR/bin/fsl_reg $g $f ${g}_to_$f -e -fnirt
>>> --inmask=${subjdir}/FA_tbss/${mysub}_lesion_mask -FA" >> .commands
>>> fi
>>> done
>>> }
>>>
>>> Did I do that incorrectly or are there other scripts I need to edit?
>>> Any advice is appreciated.
>>
>> You need to add double quotes within the call to fsl_reg. Try this
>> instead:
>>
>> do_reg(){
>> f=$1
>> for g in `$FSLDIR/bin/imglob *_FA.*` ; do
>> o=${g}_to_$f
>> mysub=`basename ${g} _FA_FA.nii.gz`
>> if [ ! -f ${o}_warp.msf ] ; then
>> echo $o
>> touch ${o}_warp.msf
>> echo "$FSLDIR/bin/fsl_reg $g $f ${g}_to_$f -e -fnirt \"--
>> inmask=${subjdir}/FA_tbss/${mysub}_lesion_mask\" -FA" >> .commands
>> fi
>> done
>> }
>>
>>
>>>
>>> Thank you,
>>> Xin
>>
>> Cheers,
>> Saad.
>>
>>
>>>
>>
>> --
>> Saad Jbabdi
>> Oxford University FMRIB Centre
>>
>> JR Hospital, Headington, OX3 9DU, UK
>> +44 (0) 1865 222545 (fax 717)
>> www.fmrib.ox.ac.uk/~saad
>>
>>
>>
>>
>>
>>
>>
>>
>
>
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