Dear FSL users
Let say I was working on a large data set that would require to adjust the tbss_3 script to run chunk-wise. What I actually need as output is a study specific mask (mean_FA_mask). Would the following be correct:
1. Create a mean across all individual in chunk
1.1. merging FA_to_target into n chunks - fslmerge -t $chunk <input>
1.2. creating a mask for each chunk - fslmaths $chunk -max 0 -Tmin -bin mean_FA_mask_$chunk -odt char
1.3. applying the mask to each chunk - fslmaths $chunk -mas mean_FA_mask_$chunk $masked_chunk
1.4. creating a mean_FA for each chunk- fslmaths $masked_chunk -Tmean mean_FA_$chunk.nii.gz
2. Merging all chunks - fslmerge -t mean_chunk input<mean_FA_$chunk.nii.gz>
3. binarise the mean_chunk fslmaths mean_chunk -max 0 -Tmin -bin study_specific_mask -odt char
Considering that the study_specific mask is a binary file it should not be affected in any way by the order of my images in each chunk I am merging, am I right?
Your help will be greatly appreciated!!
Best wishes,
Rali
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