Hoffman2:Scripts:setup subject: Difference between revisions

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After NIFTI convert, these options can be used to run FSL mcflirt, bet and melodic also diag, and mprage.
After NIFTI convert, these options can be used to run FSL mcflirt, bet and melodic also diag, and mprage.
  -d mcflirt,bet,melodic,diags,mprage:
  -d, (or --do)
   
  mcflirt : run mcflirt
  --spm: set SPM compatability
  bet      : run bet
  melodic: run melodic
  diags   : run diagnostics
  mprage: process  anatomical scans
 
Set SPM compatability
  --spm


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


Only processing data without download  
Only processing data without download
setup_subject2  -d mcflirt,bet,melodic,diags basedir subjectID
setup_subject2  -d mcflirt,bet,melodic,diags basedir subjectID
  setup_subject2  -d mprage,mcflirt,bet,melodic,diags basedir subjectID
  setup_subject2  -d mprage,mcflirt,bet,melodic,diags basedir subjectID

Revision as of 17:37, 10 May 2019

Setup_subject script usage Setup_subject2 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 other processing.


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

(If you have downloaded the data already, this option is not needed) It requires 3 argument, separated by comma(,)

 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 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
 

Set SPM compatability

--spm

Examples:

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/--spm  -d mcflirt,bet,melodic,diags,mprage  basedir subjectID

Only processing data without download

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