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For easy use of fmriprep the following code is an example of a shell (.sh) script that can be executed with qsub (the code itslef begins at #!/bin/bash). It's important that the data is in BIDS format (http://bids.neuroimaging.io/).
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In the below code, "data_home" is the directory with all your data (including your fMRI raw data in BIDS format are stored). "data_BIDS" it the directory inside of the "data_home" that has all the BIDS formatted data, "fMRI_prepped" (also inside of "data_home") is the output directory you want your data to go into, and "fMRI_prepped_interim" (also inside of "data_home") is the directory in which you would like intermediate files to be stored. "poldracklab_fmriprep_latest-2018-02-23-390394938fcc.img" is the name of the singularity container itself, and is stored in /exports/fsw.
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The license.txt file is for freesurfer and is in the /exports/fsw directory, but you should copy it to your own data_home directory in order for the following code to work. "subject_number" refers to the subjet identifier (sub-# in BIDS format), if you leave out the --participant_label flag all subjects in the data_BIDS directory will be run sequentially (not advised as it does not make optimal use of the shark's parallelization capabilities).
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Fieldmaps and slicetiming are ignored in the following code example. You can choose to include slicetiming, however the Philips scanner at the LIBC only produces 1 B0 (fieldmap) per functional image, and currently fmriprep cannot conduct inhomogeneity correction with these files.
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See the following site for more details on fmriprep itself: http://fmriprep.readthedocs.io/en/latest/usage.html
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```bash
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#!/bin/bash
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#$ -S /bin/bash
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#$ -q all.q
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#$ -N sub-005
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#$ -pe BWA 8
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#$ -l h_vmem=8g
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#$ -cwd
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#$ -j Y
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#$ -V
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#$ -m be
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module load fsl/5.0.11-shark
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module load freesurfer/5.3.0
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module load singularity/2.4.1
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singularity exec -B data_home:/scratch /exports/fsw/poldracklab_fmriprep_latest-2018-02-23-390394938fcc.img fmriprep /scratch/data_BIDS /scratch/fMRI_prepped participant -w /scratch/fMRI_prepped_interim --fs-license-file /scratch/license.txt --ignore {fieldmaps,slicetiming} --participant_label subject_number
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``` |