Hi Saad,
It doesn't output an error message, it just outputs a number. It makes
it hard to troubleshoot, but its just obvious that it didn't work
because tbss_3 complains that everything is empty.
I think I defined everything correctly now, but I still have the same
problem. Maybe there's another script I have to edit? Any advice is
appreciated.
Thanks,
Xin
On Wed, Jul 15, 2009 at 4:03 AM, Saad Jbabdi<[log in to unmask]> wrote:
> 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
>
>
|