Hello,
I ran into a similar problem and skipped the 1x1x1mm re-sampling step,
keeping the final images in 2x2x2mm MNI space. Are there any obvious
problems with using 2mm iso instead of 1mm iso?
Also, as previous posts have indicated, I have found that when avwmerge is
encountering memory problems, it is worth trying avwmerge++.
-Ryan
On Jan 29 2007, Steve Smith wrote:
>Oh, I forgot to say that if you're not running out of RAM by _too
>much_ then it might be enough to just use avwroi++ to get rid of the
>"edges" of the data, i.e. cut down the FOV in all 3 directions, apply
>the same ROI to the 4D data and the mask, and feed that into randomise.
>
>Cheers.
>
>
>
>On 29 Jan 2007, at 07:50, Steve Smith wrote:
>
>> Hi,
>>
>> If you want to do the final stats in SPM then your only option is
>> to use SnPM (permutation testing in SPM), as the other inference
>> method in SPM (Gaussian field theory) is not valid for data on the
>> TBSS skeleton. So yes you can try to feed the all_FA_skeletonised
>> data into SnPM; I don't know if this will be more memory efficient
>> than randomise - I suspect it may not be, but you can try!
>>
>> Cheers, Steve.
>>
>>
>> On 29 Jan 2007, at 05:31, Kenneth Qiu wrote:
>>
>>> Dear Stephen,
>>>
>>> Thank you for your information. I think I can't afford a new 64-
>>> bit machine and thus plan to carry out subsequent analysis using
>>> SPM. May I ask whether those *nonlinear_hr* images are in MNI
>>> space and ready to perform statistical analysis w/o spatial
>>> smoothing? Thank you very much!
>>>
>>> Best Regards,
>>> Deqiang
>>>
>>>
>>> On 1/28/07, Steve Smith <[log in to unmask]> wrote: Hi, please
>>> see previous posts on this. For this huge analysis you
>>> will need a 64-bit machine, e.g. a 64-bit linux or Mac.
>>> Cheers.
>>>
>>>
>>> On 27 Jan 2007, at 09:41, Kenneth Qiu wrote:
>>>
>>> > Dear FSLexperts,
>>> >
>>> > I'm currently using TBSS to analyze a DTI dataset with 160 images.
>>> > I have been sucessful before the last few steps of tbss_3_postreg.
>>> > When it tried to concatenate all *_nonlinear_hr.* images into one
>>> > 4D image file using avwmerge, the machine reported "out of memory"
>>> > error and the process was killed automatically. With each image
>>> > requiring 14M mem, I caculate that I would need around 2.4 G mem,
>>> > which is bigger than what I have. Therefore, I want to know whether
>>> > there is any way to bypass this obstacle, e.g not using 4D storage.
>>> >
>>> > Any comment is welcome and appreciated!
>>> >
>>> > Regards,
>>> > Deqiang
>>>
>>>
>>> ---------------------------------------------------------------------
>>> ---
>>> ---
>>> 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
>> ----------------------------------------------------------------------
>> -----
>
>
>------------------------------------------------------------------------
>---
>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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