Dear experts,
I'm trying to perform a tbss-analysis of a group of patients with suspected idiopathic normal pressure hydrocephalus and I ran into a problem (once again). We acquired for each patient a total of two decent DTI scans (MGH_sequence, 2 mm iso, 60 dir) - one before and one after lumbar drainage.
I followed the recommendations of tbss, starting with bet, eddy_correct (the age before blip up/down) and dtifit. Then I did tbss_1 and tbss_2_reg -n. The second step took about 30 to 36 hours (too bad, we don't have SGE).
After running tbss_3 I looked at the skeleton and had to find out, that in one patient the estimated skeleton runs right through the parietal part of both lateral ventricles.
I knew that I have to use a study specific template (2nd step with the -n option) but even that wasn't enough for one patient, which I truly understand looking at the raw data - this one really does have HUGE ventricles.
So my question for the interested audience is: Should I exclude the patient or can I proceed tbss?
Proceeding tbss-analysis leads me to more questions I would like to ask (and that I didn't find an answer reviewing the forum history):
I want to analyze to whole group and therefore could use the paired t-Test (ALL patients had exactly two scans). Since I also want to use co-variates (respondes positive to lumbar drainage, age, drained CSF volume) I would follow the approach suggested by Prof. Mumford: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;e8a2690f.1305
Question no1: Following this approach, I have to subtract examination 2 from examination 1 (i.e. FA_after.nii.gz minus FA_before.nii.gz). At what stage do I do that? Do I run tbss all the way up to tbss_4 and then subtract? If I do so - what about the transforms that are probably slightly different for the single examinations (before, after) performed by tbss before? Or do I perform fslmaths-subtraction right after dtifit and start tbss from the beginning?
Question no2: Having a very limited experience of statistics reading the forum and recommended sites I would demean the covariates "age" and "CSF volume" and also use the -D option in randomize. But what about the covariate "response to lumbar drainage" - actually this covariate devides the group into two subgroups - can I perfom randomize using a covariate or do I rather have to perform randomize with each subgroup for itself?
Once again, thank you very much for your kind help.
Best,
Martin
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