1MECOMBINE(1)                Generated Python Manual               MECOMBINE(1)
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NAME

6       mecombine
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SYNOPSIS

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

13       Combine multi-echo echoes.
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15       Tools to combine multiple echoes from an fMRI acquisition.  It  expects
16       input files saved as NIfTIs, preferably organised according to the BIDS
17       standard.
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19       Currently three different combination algorithms are supported,  imple‐
20       menting the following weighting schemes:
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22       1. PAID => TE * SNR 2. TE => TE 3. Simple Average => 1
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25       pattern
26              Globlike search pattern with path to select the echo images that
27              need to be combined. Because of the search,  be  sure  to  check
28              that not too many files are being read
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OPTIONS

32       -o OUTPUTNAME, --outputname OUTPUTNAME
33              File  output  name. If not a fullpath name, then the output will
34              be stored in the same folder as the input. If empty, the  output
35              filename  will be the filename of the first echo appended with a
36              '_combined' suffix
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39       -a {PAID,TE,average}, --algorithm {PAID,TE,average}
40              Combination algorithm. Default: TE
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43       -w [WEIGHTS ...], --weights [WEIGHTS ...]
44              Weights (e.g. = echo times) for all echoes
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47       -s, --saveweights
48              If passed and algorithm is PAID, save weights
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51       -v VOLUMES, --volumes VOLUMES
52              Number of volumes that is used to compute the weights  if  algo‐
53              rithm is PAID
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COMMENTS

57       examples:
58         mecombine               '/project/number/bids/sub-001/func/*_task-mo‐
59       tor_*echo-*.nii.gz'
60         mecombine                                              '/project/num‐
61       ber/bids/sub-001/func/*_task-rest_*echo-*.nii.gz' -a PAID
62         mecombine                                              '/project/num‐
63       ber/bids/sub-001/func/*_acq-MBME_*run-01*.nii.gz'  -w  11  22   33   -o
64       sub-001_task-stroop_acq-mecombined_run-01_bold.nii.gz
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AUTHOR

69       Daniel Gomez <dgomez1@mgh.harvard.edu>
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DISTRIBUTION

73       The    latest   version   of   multiecho   may   be   downloaded   from
74       ⟨https://github.com/Donders-Institute/multiecho⟩
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78multiecho 0.28                    2023-08-25                      MECOMBINE(1)
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