Oh goodness how silly of me! Yes that is much better now.
Thank you!
Steve Smith wrote:
> 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
> ------------------------------------------------------------------------
> ---
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