Hoffman2:Scripts:setup subject 3

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Setup_subject script usage

Setup_subject_3 is built on top of setup_subject_2. The major goal is to apply BIDs format on the data structure. Besides of using BIDs structure, it added other useful features as well.

Setup_subject_3 has all the functions which exist in setup_subject_2 and works the same way with the same options as setup_subject_2.


Basic Usage:

setup_subject_3 [option] basedir subjectID

basedir is where you want the processed data to be stored in your Hoffman account,

subjectID is the subject folder name which has your subject Dicom data

Options:

--download hostname,userid,path

download data from Dicom server to you hoffman account It requires 3 argument, separated by comma(,) (If you have downloaded the data already, this option is not needed)

 1. hostname - (ccn for ccn Dicom server, bmap for BMC Dicom server). 
 2. userid: Your Dicom server user ID
 3. path: path to your data in dicom server


-d (or --do) : this option to specify the processing you want to add

After NIFTI convert, these options can be used to run FSL mcflirt, bet and melodic also diag, and mprage.

  mcflirt : run mcflirt 
  bet : run bet
  melodic : run melodic
  diags : run diagnostics
  mprage : process  anatomical scans
  sge: submit the job in batch mode

(Using option diags requires mcflirt, bet and melodic to be processed first)


-s (or --skip) 

this option to specify the processing you want to skip

  mcflirt : run mcflirt 
  bet : run bet
  melodic : run melodic
  diags : run diagnostics
  mprage : process  anatomical scans
  sge: not using batch mode, which means you need to start interactive mode first before running setup_subject_* command
 
--spm

Set SPM compatability


--bids

Bids format: specify using bids structure to group result files. However this option often being used with --config option to choose configuration file. Without configuration file, the name conversion might not be correct under BIDs format rule.

Examples:

Load the script module first:

module load ccnscripts

Download data and run NIFTI convert

setup_subject_3 --download ccn,dicomuserid,/dicom/data/YOURGROUP/ basedir subjectID

( /dicom/data/YOURGROUP/subjectID should be where the raw data is located and accessable by your Dicom server user account)

Download data and run NIFTI convert and other FSL processing:

setup_subject_3 --download ccn,userid,/dicom/data/YOURGROUP/ -d mcflirt,bet,melodic,diags,mprage --spm basedir subjectID

Process data only without download

setup_subject_3 -d mcflirt,bet,melodic,diags basedir subjectID
setup_subject_3 -d mcflirt,bet,melodic,diags,mprage basedir subjectID
setup_subject_3 -d mprage basedir subjectID

Skip mcflirt,bet,melodic,diags

 setup_subject_3 -s mcflirt,bet,melodic,diags basedir subjectID

Notes

Log File: provides useful details about what commands were run, their output and the script's status. It's located at

basedir/subjectID/notes/setup_log.date_numbers