Hi Xin
Sorry I haven't noticed the rest of your modifs to do_reg()!
You need to make sure that in your version of do_reg, the variables
'mysub' and 'subjdir' are defined correctly.
It seems to me that they are not..
Also, what is the error that you get exactly?
Cheers,
Saad.
On 14 Jul 2009, at 14:03, Xin Zheng wrote:
> Hi Saad,
>
> I tried editing with the double quotes, but I basically get the same
> problem.
>
> It outputs:
>
> {subject1}_FA_FA_to_{subject2}_FA_FA (for all the subjects to each
> other)
> 24052
>
> The number seems to change each time and I find the
> tbss_2_reg.o24052.* still in my FA directory. Any ideas what else I
> should be doing?
>
> Thanks,
> Xin
>
> On Thu, Jul 9, 2009 at 12:54 PM, Saad Jbabdi<[log in to unmask]>
> wrote:
>> 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
>>
>>
>>
>>
>>
>>
>>
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
+44 (0) 1865 222523 (fax 717)
www.fmrib.ox.ac.uk/~saad
|