Dear Steve,
Thank you for all help!
Best,
Aga
On 04.10.2007 10:09 Uhr, "Steve Smith" <[log in to unmask]> wrote:
> Hi,
>
> On 4 Oct 2007, at 08:15, Agnieszka Burzynska wrote:
>
>> Hi,
>> Sorry for late response, but I was getting a visa in poland:)
>>
>> I traced back what happened and obviously 3 registartions did not
>> work, but
>> this I could see only after running tbss_3_postreg and slicesdir
>> *.nii. I
>> simply re-run the tbss_2_reg for these 3 subjects and was lucky
>> they looked
>> finally ok! Ufff...and the tbss_3 looked also reasonable. 3 questions
>> remain:
>> -how can I be sure that all other registrations are ok if running
>> the same
>> registration script twice gives different results?
>
> In a sense, it doesn't (the program is deterministic) - if it
> succeeds, then the results will always be the same - if it fails once
> and succeeds a different time, then something must have gone wrong on
> the computer before (e.g. running out of disk space, quota, RAM,
> etc.). So if it all looks ok, then that's fine.
>
> However you should always evaluate the all_FA image in FSLView, as
> described in the TBSS manual; this is a very easy way of getting a
> quick check that all the subjects were registered reasonably and in
> line with the skeleton.
>
>> -is it normal that the registered FA brain when overlaid with
>> MNI152 does
>> not overlap with it to the very edges of the MNI152 cortex?(white
>> matter is
>> well aligned, but the whole registered brain looks a bit smaller)
>
> Yes, this is normal as the FA values fall off so much once you reach
> grey matter. To get a feeling for what's "normal" you could overlay
> the standard space FMRIB58_FA image on top of the MNI152 in FSLView.
>
>> -how to adjust cluster-forming t threshold: is 1.5 also ok for my 35
>> subjects?
>
> See previous emails on this - I'm afraid there's no good answer to
> this; that's one of the weaknesses of cluster-based thresholding. 1.5
> is valid (in the sense that randomise will end up giving you valid
> corrected p-values in the maxc image, regardless of the cluster-
> forming threshold), but may not be "optimal" for your data.
>
> Cheers, Steve.
>
>
>> Thank you!
>> Best,
>> Aga
>>
>>
>>
>>
>> On 03.10.2007 10:15 Uhr, "Steve Smith" <[log in to unmask]> wrote:
>>
>>> Hi - if the initial image orientations are not axial or the images
>>> are a cut-down FOV then sometimes the IRTK registration can fail.
>>> Might this explain it?
>>>
>>> The tbss_2_reg.e12345.6 etc files are just log files so you don't
>>> need to copy them.
>>>
>>> What happens if you run
>>> fslinfo all_FA
>>> fslstats all_FA -r -R
>>> in the stats directory? Does it have the right number of timepoints?
>>>
>>> Cheers.
>>>
>>>
>>>
>>> On 1 Oct 2007, at 10:20, Agnieszka Burzynska wrote:
>>>
>>>>
>>>> Hi,
>>>> A little follow-up:
>>>> I checked all my data from the very beginning: the FA maps looks ok
>>>> as well as scaled ANALYZE files after tbss_1_preproc. 2
>>>> registrations look bad after tbss_2_reg: on one there is nothing
>>>> and on the second looks as if half of brain is cut off. I am
>>>> trying to repeat the registration for these 2 now, hoping this will
>>>> solve the problem. Do you know why so many registrations work well
>>>> but for some it doesnt work? Is there anything else that could have
>>>> gone wrong?
>>>>
>>>> Thank you!
>>>> Aga
>>>
>>>
>>> ---------------------------------------------------------------------
>>> ---
>>> ---
>>> 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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