Hoffman2:Scripts:setup subject
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 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( /dicom/data/YOURGROUP/subjectID should be where the raw data is located and accessable by your Dicom server account)
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
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