Hi all,
I'm having an issue when attempting to use the "--no_despike" flag in the meica.py script. From taking a look at the preprocessing script that meica.py spits out, it appears that in the initial t-shift block where despiking would take place, the script is adding and additional file suffix to the input file name. Below is an example that I pulled from the _meica_[subName]_e1234.sh script that meica.py gave me..
echo +* "Preliminary preprocessing of functional datasets: despike, tshift, deoblique, and/or axialize"
echo --------"Preliminary preprocessing dataset 11310.nii of TE=12ms to produce e1_ts+orig"
3dTshift -heptic -tpattern seq+z -prefix ./e1_ts+orig
11310_e1.nii.nii
and the same line when removing the "--no_despike" flag:
3dDespike -overwrite -prefix ./11310_e1_pt.nii.gz 11310_e1.nii
3dTshift -heptic -tpattern seq+z -prefix ./e1_ts+orig
11310_e1_pt.nii.gz
My exact call to meica.py is below
meica.py \
-d "11310_e[1,2,3,4].nii.gz" \
-e 12,28,44,60 \
-b 4v \
--tpattern=seq+z \
--tlrc=TT_N27+tlrc \
-a 11310_anat.nii.gz \
--no_despike \
--smooth=3 \
--keep_int \
--daw=10 \
--OVERWRITE
Thanks so much,
Mark
