Hi, no I'm afraid you can't run TBSS at 2mm resolution - that's just
too low for most tract widths, and all the validation regarding
projecting tract centre values onto the skeleton will not apply. Sorry!
On 29 Jan 2007, at 15:55, Ryan Muetzel wrote:
> 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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------------------------------------------------------------------------
---
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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