Dear Rali,
JHU-WhiteMatter-labels-1mm.nii.gz is the summary image corresponding to the labels in JHU-labels.xml, JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz is a thresholded summary image from JHU-ICBM-tracts-prob-1mm.nii.gz and corresponds to the labels in JHU-tracts.xml.
Kind Regards
Matthew
> Dear all
>
> I am interested in performing TBSS ROI. The answers I found on the mailing list have been rather confusing and I was hoping that you could confirm that what I have decided to run is indeed appropriate.
>
> I have used the following command to define the SLF (L & R):
>
> $FSLDIR/fslmaths $FSLPATH/JHU-WhiteMatter-labels-1mm.nii.gz -thr $1 -uthr $2 -mas $MASKPATH/mean_FA_skeleton_mask mask_SLF
>
> where $1 and $2 are the index taken from the JHU-labels.xml. The skeleton mask does correctly cover the ROI when displayed in fslview and the TBSS ROI results seem plausible considering initial whole-skeleton analyses. However I am confused to whether I should use the JHU-WhiteMatter-labels-1mm.nii.gz or the JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz . What is the difference?
>
> Thank you.
>
> Best wishes,
> Rali
>
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