Hi Chris,
If you email me directly, I can send you a version of probtrackx which does that.
Cheers,
Saad.
On 2 Jun 2010, at 14:44, Christian Lambert wrote:
> The output of single voxel tractography to the whole brain (define single seed, no classification mask, ventricular exclusion, usual default parameters); repeat x MANY
>
> I end off with
>
> id_region_1_1_1.nii.gz
> id_region_1_1_2.nii.gz
> id_region_1_1_3.nii.gz
> :
> etc, etc.,
>
> Is there a way to get each single output as an individual array? (i.e. Value,Location for all voxels >0))
> Thanks,
>
> - Chris
>
> Saad Jbabdi wrote:
>> Hi Chris,
>>
>> Which probtrackx output are you talking about? Is it the fdt_paths files or the target-based classification results? (i.e. seed_to_<target>.nii.gz)
>>
>> In the latter case, you can use the --s2tastext option, which will produce a ascii text file summarising the seed-to-target classification results.
>>
>> Cheers,
>> Saad.
>>
>>
>>
>>
>> On 2 Jun 2010, at 11:17, Christian Lambert wrote:
>>
>>
>>> Morning,
>>>
>>> I'm looking to change somehow my output of probtrackx. I have a bottleneck in processing which is the reading of .nii.gz files (unzip->read data->del unzipped). I have refined every other aspect of my scripts but get stuck at this point, resulting in processing times of 3-4 days + (17000-30000 files) purely from file reading (in matlab). I convert and handle all my dti data in array format for memory and speed (so purely value and location in seed source space (where value is >0) enabling simple reconstruction where required).
>>>
>>> Is there anyway to roll this into the probtrackx pipeline, maybe outputting the info as a .txt or similar?
>>>
>>> Thanks,
>>>
>>> - Chris
>>>
>>>
>>
>> --
>> Saad Jbabdi
>> University of Oxford, FMRIB Centre
>>
>> JR Hospital, Headington, OX3 9DU, UK
>> (+44)1865-222466 (fax 717)
>> www.fmrib.ox.ac.uk/~saad
>>
>>
>>
>
--
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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