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
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