Hi - it seems like maybe you're trying to run the FSL course
practical using the FEEDS data rather than the course data, which is
a separate download - see the main course website - does that solve it?
Cheers.
On 30 Jun 2007, at 14:55, Emily RUBIN-FERREIRA wrote:
> Hi Steve,
>
> Thanks for getting back to me and for clarifying about the feeds
> data. I
> will try to explain myself a bit better:
>
> The problem actually comes up when I try to go through the
> tractography
> practical - the instructions are to load FA map that I've created
> using
> DTIfit in FSLview. The file loads, but I can't scroll through the
> image
> in 3D space to find a coordinate of a voxel in the internal capsule
> (the
> FA image has only active x and y coordinates, and the z plane is
> locked
> at 0). I guess I techinically can find a voxel coordinate in the
> internal
> capsule with z=0, but I would have liked to try to seeding in another
> part of the brain, for example the superior longitudinal fasciculus.
>
> So my question is: is the example data meant to produce and FA
> map that is locked at z=0, or is there something inherently wrong
> with the
> way I've run/set up FSL/fdt so that were I to use my own data I
> would have
> a sort of truncated FA map of the brain?
>
> Thanks for your help,
> emily
>
> On Sat, 30 Jun 2007, Steve Smith wrote:
>
>> Hi - this looks ok though I'm not sure about the "errors" - I'm a
>> little confused though, as data is 2D not 3D in FEEDS.
>> Cheers.
>>
>>
>> On 29 Jun 2007, at 17:13, Emily Rubin Ferreira wrote:
>>
>>> Hi,
>>> I am trying to run DTIfit (on windows XP via cygwin) with the
>>> example data provided by the FEEDS package. I keep getting an error
>>> message:
>>>
>>> errors: 0 128 0 104 0 1
>>> 0 slices processed
>>>
>>> I checked the input data (from the folder ~/feeds/examples/
>>> fdt_subj1), to make sure they weren't corrupted, in fslview. Both
>>> input files loaded and the data.nii.gz was a complete volume but
>>> the nodif_brain_mask.nii.gz was only 2D.
>>>
>>> Attached is the fsl error report.
>>> Please let me know what I could do.
>>>
>>> Thanks,
>>> emily
>>>
>>> <fsl_By4JFW.gz>
>>
>>
>> ---------------------------------------------------------------------
>> ---
>> ---
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>> ---------------------------------------------------------------------
>> ---
>> ---
>>
------------------------------------------------------------------------
---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
------------------------------------------------------------------------
---
|