Hello,
Thank you Stephen for your prompt response,
We have done the -T option.
Now we are interested in the study specific template, so we are trying
to follow your instructions:
1) With all subjects: NC=15 and PD=37 we ran TBSS:
-tbss_1_preproc
-tbss_2_reg -S
2) Temporal copy of these results (in another folder) and delete PD=22
subjects in order to have NC=15 and PD=15:
But, which files do we have to delete?
After running tbss_1 and tbss_2, inside "FA" folder, for each subject we have:
-subject_FA(original file)
-subject_mask
-subject_to_tarjet.log
-subject_to_target_mat
-subject_to_target_warp.msf
-subject_to_target_warp.nii.gz
We have deleted all of this files from PD=22 subjects. Is it correct?
Another folder is created inside "FA": Folder tbss_logs, with some
files inside. We have not deleted files from here. We have to delete
some files from this folder too?
3) In the temporary copy, we ran:
-tbss_3_postreg -S
To get the template and skeleton:
-all_FA.nii.gz
-mean_FA.nii.gz
-mean_FA_mask.nii.gz
-mean_FA_skeleton.nii.gz
4) We copied the files created in the thirth step, into the original
folder, in a new folder "stats". Now we have to run:
-tbss_3_postreg -T (with the script amended)
How can we amend the script in order to use the templates created?
Thank you in advance,
María.
2014-09-11 7:34 GMT+02:00 Stephen Smith <[log in to unmask]>:
>
> Hi - yes it might be important for the template to not be biased - so the easiest thing to do is to use the -T option. If you think there could be value in a study-specific template, then it's a bit more complicated - probably the easiest way would be to take a temporary copy of the folder, delete 22 subjects from group 2, run the -S option to get the template and skeleton - and then go back to the original folder and run the -T option but with the script amended to use the new templates you just created.
>
> Cheers.
>
>
>
> On 9 Sep 2014, at 15:23, Maria <[log in to unmask]> wrote:
>
>> Dear Experts,
>>
>> We want to analyse DTI in FSL. We have two samples with diferent number of subjects:
>> -group 1 =14 subjects
>> -group 2 = 36 subjects
>>
>> After running tbss_1_preproc *.nii.gz and tbss_2_reg -T, which command would be more appropiate in this case?
>>
>> 1) tbss_3_postreg -S
>>
>> 2) tbss_3_postreg -T
>>
>> The diferences in the number of subjects between samples could influence the mean_FA_skeleton_mask and the all_FA_skeletonised?
>>
>> Thank you in advance,
>>
>> María.
>
>
>
> ---------------------------------------------------------------------------
> 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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>
>
>
>
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