mecombine - Man Page

mecombine [-h] [-o OUTPUTNAME] [-a {PAID,TE,average}] [-w [WEIGHTS ...]] [-s] [-v VOLUMES] pattern

Combine multi-echo echoes.

Tools to combine multiple echoes from an fMRI acquisition. It expects input files saved as NIfTIs, preferably organised according to the BIDS standard.

Currently three different combination algorithms are supported, implementing the following weighting schemes:

1. PAID => TE * SNR 2. TE => TE 3. Simple Average => 1

pattern

Globlike search pattern with path to select the echo images that need to be combined. Because of the search, be sure to check that not too many files are being read

-o OUTPUTNAME, --outputname OUTPUTNAME

File output name. If not a fullpath name, then the output will be stored in the same folder as the input. If empty, the output filename will be the filename of the first echo appended with a '_combined' suffix

-a {PAID,TE,average}, --algorithm {PAID,TE,average}

Combination algorithm. Default: TE

-w [WEIGHTS ...], --weights [WEIGHTS ...]

Weights (e.g. = echo times) for all echoes

-s,  --saveweights

If passed and algorithm is PAID, save weights

-v VOLUMES, --volumes VOLUMES

Number of volumes that is used to compute the weights if algorithm is PAID

examples:
 mecombine '/project/number/bids/sub-001/func/*_task-motor_*echo-*.nii.gz'
 mecombine '/project/number/bids/sub-001/func/*_task-rest_*echo-*.nii.gz' -a PAID
 mecombine '/project/number/bids/sub-001/func/*_acq-MBME_*run-01*.nii.gz' -w 11 22 33 -o sub-001_task-stroop_acq-mecombined_run-01_bold.nii.gz

Daniel Gomez <dgomez1@mgh.harvard.edu>

The latest version of multiecho may be downloaded from https://github.com/Donders-Institute/multiecho