Hi Saad,
For probtrackx, if I use a nifti file as my seed image, is it possible to use nifti files as classification targets? Whenever I try this probtrackx seems to hang. I have tried leaving it overnight.
If I use surface files for seed and classification targets it works fine and completes in less than an hour.
Thanks,
David
_______________________________________________
David Nobbs, Ph.D. Student
Developmental Cognitive Neuroscience Unit
UCL Institute of Child Health, 30 Guilford Street, London WC1N 1EH
+44 (0)20 7905 2738
uk.linkedin.com/pub/david-nobbs/48/2a/674
On 12 Jun 2013, at 18:39, Saad Jbabdi wrote:
> Hi
> This is a bug in surf2surf. It doesn't save scalar information when converting to VTK. We will fix this, Thanks!
>
> in the meantime, you can use the attached matlab functions:
>
> x=surfread('file.asc');
> surfwrite(x,'file.vtk','vtk');
>
> Then you can load the output in fslview 3D mode and it should show you the clusters.
>
> Cheers
> Saad
>
>
>
>
>
> On 12 Jun 2013, at 09:33, David Nobbs <[log in to unmask]> wrote:
>
>> Hi FSL users,
>>
>> I have been through the instructions for Connectivity-Based Seed Classification, using a surface gii file of the thalamus as my seed, have run find the biggest and generated an ascii file (I have pasted the first few lines of the file below). How do I open this file in FSLVIEW so it will show the segmentations of the seed region?
>>
>> I have tried converting it into an nii file with first_utils which I can open in the Ortho view. And also to a vtk file with surf2surf which I can open in 3D view. But neither nii or vtk show the segmentations, it just appears as an unsegmented thalamus.
>>
>> Thank you for your help,
>> David
>>
>> #!ascii from CsvMesh
>> 642 1280
>> 126.1 139.341 70.2318 1
>> 124.72 139.191 87.0523 2
>> 141.219 134.43 82.6425 2
>> 141.387 133.177 64.6051 2
>> 136.613 146.438 68.5776 1
>>
>
> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466 (fax 717)
> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
>
> <surfwrite.m><surfread.m>
