squirrel utilities
The squirrel command line program
The squirrel command line program allows converstion of DICOM to squirrel, BIDS to squirrel, modification of existing squirrel packages, and listing of information from packages.
Installing squirrel utilities
Download squirrel from https://github.com/gbook/squirrel/releases
sudo yum localinstall --nogpgcheck squirrel-xxx.xx.xxx-1.elx.x86_64.rpm
Basic Command Line Usage
Convert DICOM to squirrel
# Default DICOM to squirrel conversion
squirrel dicom2squirrel /path/to/dicoms outPackgeName.sqrl
# Specify the output format
squirrel dicom2squirrel /path/to/dicoms outPackge.sqrl --dataformat niti4gz
# Specify the package directory format
squirrel dicom2squirrel /path/to/dicoms outPackage.sqrl --dirformat seq
Convert BIDS to squirrel
squirrel bids2squirrel /path/to/bids outPackage.sqrl
Modify existing squirrel package
# add a subject to a package
squirrel modify /path/to/package.sqrl --add subject --datapath /path/to/new/data --objectdata 'SubjectID=S1234ABC&DateOfBorth=199-12-31&Sex=M&Gender=M'
# remove a study (remove study 1 from subject S1234ABC)
squirrel modify /path/to/package.sqrl --remove study --subjectid S1234ABC --objectid 1
List information about a squirrel package
#list package information
[user@hostname]$ squirrel info ~/testing.sqrl
Squirrel Package: /home/nidb/testing.sqrl
DataFormat: orig
Date: Thu May 23 16:16:16 2024
Description: Dataset description
DirectoryFormat (subject, study, series): orig, orig, orig
FileMode: ExistingPackage
Files:
314 files
19181701506 bytes (unzipped)
PackageName: Squirrel package
SquirrelBuild: 2024.5.218
SquirrelVersion: 1.0
Objects:
├── 8 subjects
│ ├── 8 measures
│ ├── 0 drugs
│ ├── 11 studies
│ ├──── 314 series
│ └──── 0 analyses
├── 0 experiments
├── 0 pipelines
├── 0 group analyses
└── 0 data dictionary
# list subjects
[user@hostname]$ squirrel info ~/testing.sqrl --object subject
Subjects: sub-ASDS3050KAE sub-ASDS6316BWH sub-ASDS6634GJK sub-ASDS7478SKA sub-ASDS8498GQDCBT sub-HCS8276XPS sub-S4328FSC sub-S7508DDH
# list studies for a specific subject
[user@hostname]$ squirrel info ~/testing.sqrl --object study --subjectid sub-ASDS3050KAE
Studies: 1 2
#list all subjects as CSV format
[user@hostname]$ squirrel info ~/testing.sqrl --object subject --csv
ID, AlternateIDs, DateOfBirth, Ethnicity1, Ethnicity2, GUID, Gender, Sex
"sub-ASDS3050KAE","","","","","","U","U"
"sub-ASDS6316BWH","","","","","","U","U"
"sub-ASDS6634GJK","","","","","","U","U"
"sub-ASDS7478SKA","","","","","","U","U"
"sub-ASDS8498GQDCBT","","","","","","U","U"
"sub-HCS8276XPS","","","","","","U","U"
"sub-S4328FSC","","","","","","",""
"sub-S7508DDH","","","","","","",""
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