Hoffman2:Scripts:setup subject

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Setup_subject script usage

Setup_subject2 (replaced setup_subject) is used to download data from Dicom server and run NIFTI convert on the subject data. Other options such as mcflirt, bet, melodic, diags or mprage can be specified to run FSL processing and others.


Basic Usage:

setup_subject2 [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 : This option will 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. Your Dicom server user ID
 3. Path to your data in dicom server

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

-d (or --do) 
  mcflirt : run mcflirt 
  bet : run bet
  melodic : run melodic
  diags : run diagnostics
  mprage : process  anatomical scans

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

Set SPM compatability

--spm

Examples:

Load the script module first:

module load ccnscripts

Download data and run NIFTI convert

setup_subject2 --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_subject2 --download ccn,userid,/dicom/data/YOURGROUP/ -d mcflirt,bet,melodic,diags,mprage --spm basedir subjectID

Process data only without download

setup_subject2 -d mcflirt,bet,melodic,diags basedir subjectID
setup_subject2 -d mcflirt,bet,melodic,diags,mprage basedir subjectID
setup_subject2 -d mprage 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