Thanks.. I may try that if the HCP data gives unexpected results.
Regarding this, do you know a parameter setting that is known to work
well with the HCP data?
Also, this may be a silly question, but how can I tell whether bedpostx
is running on the CPU or GPU? I do have a Tesla GPU in my machine and I
ran the command without the "-c" option, but the output is not very
verbose so it is difficult to tell if it is running on the GPU or CPU. I
assume the speed is an indication. It processed 10 slices in the last hour.
Best,
Martin
On 03/12/14 09:41, Stamatios Sotiropoulos wrote:
> Hi Martin
>
> If you haven’t try bedpostx before, it will probably make your life easier to try it first on some standard data of more typical spatial and angular resolution.
>
> Cheers
> Stam
>
>
>
> On 12 Mar 2014, at 13:35, Martin Luessi <[log in to unmask]> wrote:
>
>> Hi Moises, Stam,
>>
>> Thanks a lot. It seems to be working with the suggested parameters. I
>> plan to run it on a GPU cluster; I had added the -c flag because I
>> thought it may be easier to get it to work on the CPU first.
>>
>> Best,
>>
>> Martin
>>
>> On 03/12/14 05:59, Stamatios Sotiropoulos wrote:
>>> Hi Martin,
>>>
>>> Just to add to Moises recommendation, bedpostx on HCP data can take many hours, even on a cluster. We use the recent GPU version of bedpostx for the HCP data on a GPU cluster that allows accelerations of two orders of magnitude.
>>>
>>> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0061892
>>>
>>> Cheers
>>> Stam
>>>
>>>
>>>
>>>
>>> On 11 Mar 2014, at 21:48, Moises Hernandez Fernandez <[log in to unmask]> wrote:
>>>
>>>> Hi Martin,
>>>>
>>>> could you try to change the way you set the parameters ?
>>>>
>>>> bedpostx /hcp_data/100307/T1w/Diffusion -n 3 -b 1000 -model 2 -w 1 -g -c
>>>>
>>>> Cheers,
>>>> Moises
>>>
>>>
>>
>>
>>
>>
>>
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--
Martin Luessi, Ph.D.
Research Fellow
Department of Radiology
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Harvard Medical School
149 13th Street
Charlestown, MA 02129
Fax: +1 617 726-7422
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