Hi
You need to transform your label files to surface files as explained here: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Label_files
Cheers
Saad
On 13 Sep 2012, at 00:26, Alistair Perry wrote:
> I have all the working parts:
>
> - DTI image registered to freesurfer image using bbregister and flirt.
> From here I have created a transformation and inverse matrix
> - I have used mri_annotation2label to generate a label for each
> cortical ROI of the aparc parcellation (so I have 68)..
>
> Now, the part I do not understand is the ascii text file list of the
> volumes and/or surfaces. Is this merely just a list of the labels?
>
> For example:
>
> lh.bankssts.label
> lh.caudalanteriorcingulate.label
>
> Thanks,
>
> Alistair
>
> On Fri, Sep 7, 2012 at 11:59 PM, Saad Jbabdi <[log in to unmask]> wrote:
>> Hi Alistair
>>
>> This should now be explained better in the new FSL5 doc (released yesterday). Please have a look at the freesurfer section and let me know if you have issues.
>>
>> saad
>>
>> On 5 Sep 2012, at 04:23, Alistair Perry wrote:
>>
>>> Hello FSL experts,
>>>
>>> I know this has been posted elsewhere with the original probtrackx.
>>>
>>> I am basically trying to create a surface file from the aseg+aparc.mgz cortical parcellation created when running recon-all. I wish to use this surface file as the seed reference file when performing probtrackx2.
>>>
>>> I have succeeded sucessfully in transforming the cortical parcellation into diffusion space, and have created a label file for it.
>>>
>>> However, I am having difficulty understanding converting the label file into ascii format, as required for probtrackx2. I am aware that you can convert a label file into ascii format using mri_convert, but you have to specify the lh.white surface file created when performing recon-all. This does not make sense to me for one this label file is not in diffusion space. Plus, why would I only specify one surface hemisphere when I have a label file that lists vertices across both hemispheres?
>>>
>>> In the end I am asking whether it is possible/and the best method in creating an ascii surface file of the whole cortical parcellation in diffusion space?
>>>
>>> Regards,
>>>
>>> Alistair
>>>
>>
>> --
>> Saad Jbabdi
>> University of Oxford, FMRIB Centre
>>
>> JR Hospital, Headington, OX3 9DU, UK
>> (+44)1865-222466 (fax 717)
>> www.fmrib.ox.ac.uk/~saad
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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