Hoffman2:Scripts:setup subject: Difference between revisions
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==Setup_subject script usage== | |||
Setup_subject_2 (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 | Other options such as mcflirt, bet, melodic, diags or mprage can be specified to run FSL processing and others. | ||
==Basic Usage:== | ===Basic Usage:=== | ||
setup_subject_2 [option] basedir subjectID | |||
basedir is where you want the processed data to be stored in your Hoffman account | 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 | |||
subjectID is the subject folder name which has your subject Dicom data | |||
===Options:=== | ===Options:=== | ||
--download : This option will download data from Dicom server to you hoffman account | --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) | (If you have downloaded the data already, this option is not needed) | ||
1. Hostname - (ccn for ccn Dicom server, bmap for BMC Dicom server). | 1. Hostname - (ccn for ccn Dicom server, bmap for BMC Dicom server). | ||
2. Your Dicom server user ID | 2. Your Dicom server user ID | ||
3. Path to your data in dicom server | 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. | After NIFTI convert, these options can be used to run FSL mcflirt, bet and melodic also diag, and mprage. | ||
-d (or --do) | -d (or --do) : this option to specify the processing you want to add | ||
mcflirt : run mcflirt | mcflirt : run mcflirt | ||
bet | bet : run bet | ||
melodic: run melodic | melodic : run melodic | ||
diags : run diagnostics | diags : run diagnostics | ||
mprage: process anatomical scans | 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 | Set SPM compatability | ||
| Line 30: | Line 43: | ||
===Examples: === | ===Examples: === | ||
Load the script module first: | |||
module load ccnscripts | |||
Download data and run NIFTI convert | Download data and run NIFTI convert | ||
setup_subject_2 --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: | 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 | |||
Latest revision as of 16:44, 3 July 2019
Setup_subject script usage
Setup_subject_2 (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_subject_2 [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_2 --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