Difference between revisions of "Hoffman2:Scripts:setup subject 3"

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(Setup_subject script usage)
(Setup_subject script usage)
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==Setup_subject script usage==
 
==Setup_subject script usage==
Setup_subject_3 is built on top of setup_subject_2. The major target is to apply BIDs format on the data structure.  
+
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.
 +
 
 
It has all the functions which exist in setup_subject_2 and works the same if you don't specify BIDs mode.
 
It has all the functions which exist in setup_subject_2 and works the same if you don't specify BIDs mode.
  

Revision as of 23:24, 15 October 2019

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.

It has all the functions which exist in setup_subject_2 and works the same if you don't specify BIDs mode.


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 : 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) : this option to specify the processing you want to add
  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
 

Set SPM compatability

--spm

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_2 --download ccn,userid,/dicom/data/YOURGROUP/ -d mcflirt,bet,melodic,diags,mprage --spm basedir subjectID

Process data only without download

setup_subject_2 -d mcflirt,bet,melodic,diags basedir subjectID
setup_subject_2 -d mcflirt,bet,melodic,diags,mprage basedir subjectID
setup_subject_2 -d mprage basedir subjectID

Skip mcflirt,bet,melodic,diags

 setup_subject_2 -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