Dear Mark,
thanks a lot for your advice!
Best,
Sebastian
On 27.01.2013 02:17, Mark Jenkinson wrote:
> Hi,
>
> If you've defined your lesion masks on the original images (as you
> normally would) then just add the --inmask options. For running
> randomise we would recommend the new setup_masks tool, as this is really
> what it was designed to do.
>
> All the best,
> Mark
>
>
> On 23 Jan 2013, at 09:58, "Papazoglou, Sebastian"
> <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
>> Hi Gwenaëlle,
>>
>> Thanks a lot for your quick reply! According to the previous posts I
>> will need to edit the call to fsl_reg in the fslvbm_2 and fsl_vbm_3
>> scripts.
>> Two of the three fsl_reg calls in the scripts seem to pass options
>> onto FNIRT (--config and --jout) - so do I have to add --inmask to
>> these options together with an inverted lesion mask?
>> And would you recommend using the new setup_masks tool in the
>> randomise step?
>>
>> Many thanks for your help!
>> Best,
>> Sebastian
>>
>> Am 22.01.2013 um 19:06 schrieb Gwenaëlle DOUAUD:
>>
>>> Hi,
>>>
>>> this has been discussed previously on the list. Please have a look at
>>> the archives (https://www.jiscmail.ac.uk/cgi-bin/webadmin) with the
>>> relevant keywords (e.g., vbm and lesion) and adding for instance my
>>> email address as an advanced option for the search.
>>>
>>> Cheers,
>>> Gwenaëlle
>>> --------------------------------------------------------------------
>>> Gwenaëlle Douaud, PhD
>>> FMRIB Centre, University of Oxford
>>> John Radcliffe Hospital, Headington
>>> OX3 9DU Oxford UK
>>> Tel: +44 (0) 1865 222 523
>>> Fax: +44 (0) 1865 222 717
>>> www.fmrib.ox.ac.uk/~douaud <http://www.fmrib.ox.ac.uk/~douaud>
>>> --------------------------------------------------------------------
>>> ------------------------------------------------------------------------
>>> *De :* Sebastian Papazoglou <[log in to unmask]
>>> <mailto:[log in to unmask]>>
>>> *À :* [log in to unmask] <mailto:[log in to unmask]>
>>> *Envoyé le :* Mardi 22 janvier 2013 17h05
>>> *Objet :* [FSL] fslvbm including lesion masks
>>>
>>> Dear FSL-Experts,
>>>
>>> Is there an option (or a way) in FSl 5 to run an fslvbm using WM
>>> lesion masks?
>>>
>>> Many thanks in advance!
>>> Best regards,
>>> Sebastian
>>>
>>>
>>
>> ----
>> Dr. rer. nat. Sebastian Papazoglou
>> Post Doctoral Research Fellow
>> Charité- University Medicine Berlin
>> NeuroCure- Clinical Research Center
>> Charitéplatz 1
>> 10117 Berlin
>> Germany
>>
>> Tel. +49-30-450-539797
>> Fax. +49-30-450-539915
>>
>> [log in to unmask] <mailto:[log in to unmask]>
>>
>>
>>
>>
>>
>>
>
--
Dr. rer. nat. Sebastian Papazoglou
Post Doctoral Research Fellow
Department of Radiology
Charité University Medicine
Charitéplatz 1
10177 Berlin
Germany
Tel. +49-30-450-539118
Fax. +49-30-450-539998
[log in to unmask]
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