FMRI: Difference between revisions
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| Line 6: | Line 6: | ||
<code> | <code> | ||
-d 'echo[1,2,3].nii' | -d 'echo[1,2,3].nii' | ||
-a 'brainmask.nii' | -a 'brainmask.nii' | ||
-e 13.0,30.55,48.1 | -e 13.0,30.55,48.1 | ||
--TR=2.43 | --TR=2.43 | ||
--tpattern=seq-z | --tpattern=seq-z | ||
-b 15s | -b 15s | ||
--fres=2.5 | --fres=2.5 | ||
--mask_mode='anat' | --mask_mode='anat' | ||
--no_skullstrip --OVERWRITE | --no_skullstrip --OVERWRITE | ||
</code> | </code> | ||
Revision as of 11:24, 10 May 2018
MEICA and Tedana
The following pipeline describes processing steps for multi-echo ICA (ME-ICA) data, as agreed by Manfred, Frantisek and others in May 2018. This is the pipeline applied to NSPN and BioDep projects.
The ME-ICA script to be run is located on the BCNI server at: "/home/rr480/Code/MATLAB/fMRI/MEICA/meica_manfred_2018_05_10/meica.py". This includes the following options (some of which are specific to NSPN data):
-d 'echo[1,2,3].nii'
-a 'brainmask.nii'
-e 13.0,30.55,48.1
--TR=2.43
--tpattern=seq-z
-b 15s
--fres=2.5
--mask_mode='anat'
--no_skullstrip --OVERWRITE
