[Neuroimaging] nibabel.trackvis.read error

[Matthew Brett]

On Fri, Sep 4, 2015 at 10:12 PM, Matthew Brett <matthew.brett at gmail.com> wrote:
> Hi,
>
> On Fri, Sep 4, 2015 at 11:18 PM, Matthew Brett <matthew.brett at gmail.com> wrote:
>> Hi,
>>
>> On Fri, Sep 4, 2015 at 12:27 PM, C.D. Langen <c.langen at erasmusmc.nl> wrote:
>>> Hi Matthew,
>>>
>>> Thank you for your quick reply. Below are links to two datasets, one
>>> that failed to be read by nib.trackvis, and one that succeeded. Both can
>>> be viewed in Trackvis:
>>>
>>> https://dl.dropboxusercontent.com/u/57089115/fail.trk
>>> https://dl.dropboxusercontent.com/u/57089115/succeed.trk
>>>
>>> Best,
>>> Carolyn
>>>
>>> On 03-09-15 19:31, Matthew Brett wrote:
>>>> Hi,
>>>>
>>>> On Thu, Sep 3, 2015 at 10:22 AM, C.D. Langen <c.langen at erasmusmc.nl> wrote:
>>>>> Greetings,
>>>>>
>>>>> When I try to run the following line of code:
>>>>>
>>>>> streams, hdr = nib.trackvis.read(os.path.join(subjDir, 'dti.trk'),
>>>>> points_space='voxel')
>>>>>
>>>>> I get the following error, but only for a small subset of subjects:
>>>>>
>>>>>     File
>>>>> "/cm/shared/apps/python/2.7.6/lib/python2.7/site-packages/nibabel/trackvis.py",
>>>>> line 223, in read
>>>>>       streamlines = list(streamlines)
>>>>>     File
>>>>> "/cm/shared/apps/python/2.7.6/lib/python2.7/site-packages/nibabel/trackvis.py",
>>>>> line 202, in track_gen
>>>>>       buffer = pts_str)
>>>>> TypeError: buffer is too small for requested array
>>>>>
>>>>>
>>>>> Someone else had a similar error
>>>>> (http://mail.scipy.org/pipermail/nipy-devel/2012-March/007272.html)
>>>>> which they resolved by using nibabel from github. I tried this, but got
>>>>> the same error.
>>>>>
>>>>> All subjects' trackvis files were produced in exactly the same way using
>>>>> Trackvis, so I am not sure why only a few subjects fail while others
>>>>> succeed. Any ideas?
>>>>>
>>>>> Thank you in advance for your help in resolving this issue.
>>>> Thanks for the report - would you mind put the file online somewhere
>>>> so we can have a look?
>>
>> What seems to be happening is that the last track in the file is
>> truncated.  It says that it is 120 points long (n_pts field), but
>> there is only data in the file for 77 points.
>>
>> I tried reading the file with this MATLAB toolbox :
>> https://github.com/johncolby/along-tract-stats
>>
>>>> [header, tracks] = trk_read('fail.trk');
>>>> tracks(end)
>>
>> ans =
>>
>>     nPoints: 120
>>      matrix: [77x3 single]
>>
>>>> tracks(end-1)
>>
>> ans =
>>
>>     nPoints: 91
>>      matrix: [91x3 single]
>>
>> Note that the last track has 120 'nPoints' but only 77 points.  The
>> previous track has 91 'nPoints' and 91 points, which is what I would
>> expect.  So I think the file is mal-formed and trackvis is being more
>> generous than nibabel.  I think nibabel should have a mode where it
>> passes through this kind of thing.   In the meantime, if you want to
>> read all but the last shortened track, you could do something like
>> this:
>>
>> import nibabel as nib
>>
>> track_gen, hdr = nib.trackvis.read('fail.trk', as_generator=True)
>>
>> tracks = []
>> while True:
>>     try:
>>         track = next(track_gen)
>>     except (StopIteration, TypeError):
>>         break
>>     tracks.append(track)
>
> I put up a potential fix here : https://github.com/nipy/nibabel/pull/346
>
> If merged, this will allow the following:
>
> tracks, hdr = nib.trackvis.read('fail.trk', errors='lenient')

It's merged now, so I think the current github version of nibabel will
read your file correctly,

Best,

Matthew