Hi Matthew,
I am running FSL version 4.1.4.
I should elaborate on my processing pipeline, since it is complicated. I have specific questions below, marked with ***. Thank you so much for your time.
-I am running all TBSS steps on a quadcore MacPro running OX 10.5.8
-The sample is a between-group design of toddlers N=77, clinical vs. controls.
-I originally ran tbss_2_reg -n (flag), and it completed after 17 days without crashing.
-I ran tbss_3_postreg -S (flag), and then I checked the alignment of all_FA under mean_FA_skeleton.
-I discovered that every volume (0-76) of all_FA had a large signal dropout in the right superior frontal lobe. The mean_FA_skeleton also had this artifact.
-After some investigation, I found that the FA map for 1 single clinical subject had this artifact. I assumed that this one subject was causing all the volumes of all_FA and the mean_FA_skeleton to have this artifact.***
-Rather than removing the 1 subject from the start and re-running tbss_2_reg for another 17 days, I tried the following: I removed all files written during tbss_3_postreg and then removed all files that were written during tbss_2_reg that contained the file name of the faulty subject (i.e. all the nonlinear warps created from the faulty subject during tbss_2_reg).***
-I then ran tbss_3_postreg again, and now every volume of the new all_FA (0-75) did not have the artifact, and neither did mean_FA_skeleton.
-Thus, I proceeded with tbss_4_prestats 0.2 (threshold) and ran randomise with the --T2 (TFCE flag).
-The corrected (corrp) statmap did not show any significant group differences, even at very low (1-p=.60) threshold.***
-Then I tried running RD and AD and received the error I detailed in my earlier post.***
***Questions:
1) Is it possible that 1 faulty subject with artifact could apply this artifact to all other subjects during tbss_2_reg and tbss_3_postreg?
2) Is it possible to remove a subject (and all associated files) from a TBSS analysis after tbss_2_reg has already ran?
3) Could my troubleshooting attempt affected the statistical analysis and power to detect differences?
4) Could running tbss_non_FA give an error because of my troubleshooting attempt to remove a subject after tbss_2_reg?
Thank you so much for your help.
Mark Shen
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