Hi Prantik,

Thanks for your advice. I have multi echo rat data acquired on 4,7 T scanner and I was using kdaw = 50-60 and rdaw = 1-5. I followed your lead and I tried running the preprocessing from your script. My data is in talairach space and when the parameters for the first echo are calculated it saves the file as e1_ts+orig.BRIK and proceeds but while processing the second echo it saves the file as e2_ts+tlrc.BRIK and obviously its not able to load the +orig file which gives me an error

++ 3dWarp: AFNI version=AFNI_2011_12_21_1014 (Jul 18 2014) [64-bit]
++ Authored by: RW Cox
** FATAL ERROR: Can't open dataset ./e2_ts+orig

I discovered that this happens during despiking so I used --no_despike which leads to this.

++ 3dTshift: AFNI version=AFNI_2011_12_21_1014 (Jul 18 2014) [64-bit]
** FATAL ERROR: Can't open input dataset!

I managed to solve it by changing the input of the 3dTshift and the script runs fine but I while running tedana I am getting an error

  Rhos_elbow = np.mean([Rhos_lim[getelbow(Rhos_lim)]  , Rhos_sorted[getelbow(Rhos_sorted)], getfbounds(ne)[0]])
  File "/Users/User/abin/meica.libs/tedana.py", line 311, in getelbow
    p  = coords - np.tile(np.reshape(coords[:,0],(2,1)),(1,nc))
IndexError: index 0 is out of bounds for axis 1 with size 0

I belive that there is a problem with finding the rho elbow (Increasing rdaw in some cases solves the problem).

Do you have any other advices?

I am running meica.py -d raw_e1.nii,raw_e2.nii,raw_e3.nii,raw_e4.nii,raw_e5.nii -e 8.23,16.43,24.63,32.83,41.03 --smooth 0.4 --tpattern alt+z --OVERWRITE --TR 2 --no_despike --daw 60

PS. I tried adding --tlrc but it is not solving the problem

Best,
John