Hello,
I haven’t seen any discussions on fmriprep+mutliecho+tedana for a while, has there be any movements in combining fmriprep and tedana?
For now, my approach is to use fmriprep on individual echo, then feed them to tedana.
I saw in some previous posts about using --echo-idx to prevent fmriprep from combining all echoes. But if you have three echoes, you can’t use --echo-idx 1 2 3. What is the proper argument when you have three echoes in func?
BTW,
My func folder consists of (plus corresponding json files):
sub-026_ses-01brain_task-heat_acq-gatedResampled_rec-RetroicorSliceTime_echo-1_bold.nii
sub-026_ses-01brain_task-heat_acq-gatedResampled_rec-RetroicorSliceTime_echo-2_bold.nii
sub-026_ses-01brain_task-heat_acq-gatedResampled_rec-RetroicorSliceTime_echo-3_bold.nii
Using the following command seems to combine all the echoes:
PYTHONPATH="" singularity run
-B {MYPATH}/sub-026a/data:/data \
-B {MYPATH}/sub-026a/output:/output
-B {MYPATH}/sub-026a/work:/work \
-B {HOME}/license.txt:/license.txt
/share/PI/russpold/singularity_images/poldracklab_fmriprep_20.1.2-2020-09-04-e8e4a3cb1157.simg
/data /output participant --participant-label sub-026
-w /work --fs-license-file /license.txt
–mem-mb 64000 --nthreads 10 --ignore ‘slicetiming’
–output-spaces MNI152Lin:res-2
–use-aroma -v
Christine