That script was written for an earlier version of fsl. The updated script
would be:
fslmerge -t big4d data1 data2 #merge the averages into a single 4D file
bash eddy_correct big4d big4d_corr 0 #motion correct all data to first
volume
bash -c "fslroi big4d_corr av1_corr 0 40"
bash -c "fslroi big4d_corr av2_corr 40 40"
fslmaths av1_corr -add av2_corr -div 2 data #average motion corrected
data
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Siewmin Gan
Sent: Tuesday, March 10, 2009 6:01 AM
To: [log in to unmask]
Subject: [FSL] script to average dti data.
Hi Matt,
I found this very useful script you wrote in 2007 :). I have
seperated my 2 sets of dt with the fslroi commands you wrote. I tried the
last line using fslmaths_32R .... but it says command not found. May I ask
what 32R stands for?
Would it be right if I use fslmaths av1_corr -add av2_corr -div 2 data for
the last step to average 2 repeat of dti 30 dir 5 b0? I checked my output
results and the values in the output image voxels is the average of the 2
repeat dti.
avwmerge -t big4d data1 data2 #merge the averages into a single 4D file
bash eddy_correct big4d big4d_corr 0 #motion correct all data to first
volume
bash -c "avwroi big4d_corr av1_corr 0 40"
bash -c "avwroi big4d_corr av2_corr 40 40"
avwmaths_32R av1_corr -add av2_corr -div 2 data #average motion corrected
data
Many Thanks in advance
Siewmin
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