Hi Gwenaëlle
I had also done a nonlinear registration (tbss_2_reg -t
own_template.nii.gz). But when running tbss_3_postreg -S, the affine
transform is done onto the MNI152 T1 template. I changed the tbss_3_postreg
script so that it uses our customized template instead of the MNI152 T1
template.
Thanks a lot
Regards
Jürgen
On [DATE], "Gwenaëlle DOUAUD" <[ADDRESS]> wrote:
> Hi Jürgen,
>
> just a question: are you sure you want to do only an affine registration?
> I am really unsure whether this would be enough to align, at least roughly,
> the tracts across subjects so that the centre of them would be picked up and
> projected onto the skeleton...
>
> If you're happy to go with a non-linear registration, then tbss_2_reg -t
> followed by tbss_3_postreg -S should do the trick.
>
> Cheers,
> Gwenaelle
>
>
> --- En date de : Mer 27.5.09, Jürgen Hänggi <[log in to unmask]> a
> écrit :
>
>> De: Jürgen Hänggi <[log in to unmask]>
>> Objet: Re: [FSL] Tbss_3_postreg and own template
>> À: [log in to unmask]
>> Date: Mercredi 27 Mai 2009, 11h08
>> Hi Steve
>>
>> Thanks a lot
>>
>> Regards
>> Jürgen
>>
>>
>> On [DATE], "Steve Smith" <[ADDRESS]> wrote:
>>
>>> Sure - just edit the scripts! They're quite
>> straightforward. Cheers
>>>
>>> --------------------
>>> Stephen M. Smith, Professor of Biomedical
>> Engineering
>>> Associate Director, Oxford University
>> FMRIB Centre
>>>
>>> FMRIB, JR Hospital, Headington,
>>> Oxford. OX3 9 DU, UK
>>> +44 (0) 1865 222726 (fax 222717)
>>> [log in to unmask]
>>> http://www.fmrib.ox.ac.uk/~steve
>>> ----------------------
>>>
>>> On 27 May 2009, at 06:54, Jürgen Hänggi
>>> <[log in to unmask]>
>> wrote:
>>>
>>>> Dear FSL experts
>>>>
>>>> We created a DTI template that includes the whole
>> brain stem and the
>>>> upper
>>>> part of the spinal cord and would like to affine
>> register the FA
>>>> maps on
>>>> this template (instead of the MNI152 template)
>> using the
>>>> tbss_3_postreg
>>>> script.
>>>>
>>>> Is there a possibility to force tbss_3_postreg to
>> use our customized
>>>> template instead of the MNI152 template, or should
>> I do that with
>>>> FLIRT?
>>>>
>>>> Thanks in advance
>>>> Best regards
>>>>
>>>> Jürgen
>>>>
>>>> ---
>>>> ---
>>>>
>> ----------------------------------------------------------------------
>>>> Juergen Haenggi
>>>> Ph.D. (Dr. des.)
>>>> Division Neuropsychology
>>>> Institute of Psychology
>>>> University of Zurich
>>>> Binzmuehlestrasse 14, PO Box 25
>>>> 8050 Zurich, Switzerland
>>>> 0041 44 635 73 97 (phone office)
>>>> 0041 76 445 86 84 (phone mobile)
>>>> 0041 44 635 74 09 (fax office)
>>>> BIN 4.D.04 (office room number)
>>>> j.haenggi[at]psychologie.uzh.ch (email)
>>>> http://www.psychologie.uzh.ch/neuropsy/
>> (website)
>>>> http://www.juergenhaenggi.ch (private
>> website)
>>>>
>>>> This e-mail (and any attachment/s) contains
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>> ----------------------------------------------------------------------
>>>>
>>
>>
>> ----------------------------------------------------------------------------
>> Juergen Haenggi
>> Ph.D. (Dr. des.)
>> Division Neuropsychology
>> Institute of Psychology
>> University of Zurich
>> Binzmuehlestrasse 14, PO Box 25
>> 8050 Zurich, Switzerland
>> 0041 44 635 73 97 (phone office)
>> 0041 76 445 86 84 (phone mobile)
>> 0041 44 635 74 09 (fax office)
>> BIN 4.D.04 (office room number)
>> j.haenggi[at]psychologie.uzh.ch (email)
>> http://www.psychologie.uzh.ch/neuropsy/
>> (website)
>> http://www.juergenhaenggi.ch (private website)
>>
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>
>
>
----------------------------------------------------------------------------
Juergen Haenggi
Ph.D. (Dr. des.)
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
e-mail in error) please notify the sender immediately and destroy this
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