/
/squirrel.json
/data
/data/S1234ABC
/data/S1234ABC/5
/data/S1234ABC/5/1
/data/S1234ABC/5/1/S1234ABC_5_1_00001.nii.gz
/data/S1234ABC/5/2
/data/S1234ABC/5/2/S1234ABC_5_1_00001.nii.gz
/data/S1234ABC/5/3
/data/S1234ABC/5/3/S1234ABC_5_1_00001.nii.gz
/pipelines
/pipelines/freesurfer
/pipelines/freesurfer/pipeline.json

{
    "_package": {
        "NiDBversion": "version2022.5.805",
        "datetime": "2022-05-10 14:04:02",
        "description": "more details...",
        "format": "squirrel",
        "name": "pineapples",
        "version": "1.0"
    },
    "pipelines": [
        {
            "createDate": "Mon Apr 6 14:26:18 2020",
            "desc": "freesurfer for all structural T1s",
            "level": 1,
            "name": "freesurferUnified6"
        }
    ],
    "subjects": [
        {
            "ID": "S1234ABC",
            "alternateIDs": [ "ID_001", "ID_009" ],
            "dateOfBirth": "1990-04-29",
            "ethnicity1": "",
            "ethnicity2": "",
            "gender": "U",
            "sex": "U",
            "studies": [
                {
                    "ageAtStudy": 0,
                    "analysis": [
                        {
                            "clusterEndDate": "2018-02-28 02:19:22",
                            "clusterStartDate": "2018-02-26 15:37:32",
                            "diskSize": 312055410,
                            "endDate": "2018-03-09 11:53:36",
                            "hostname": "compute19",
                            "isBad": false,
                            "isComplete": true,
                            "notes": "",
                            "numSeries": 1,
                            "pipelineName": "freesurfer",
                            "pipelineVersion": 14,
                            "startDate": "2018-02-26 15:36:35",
                            "status": "complete",
                            "statusmessage": "Supplement processing complete"
                        }
                    ],
                    "dayNumber": "",
                    "description": "",
                    "modality": "MR",
                    "series": [
                        {
                            "number": 1,
                            "numfiles": 3,
                            "path": "S1234ABC/5/1",
                            "size": 303300
                        },
                        {
                            "number": 2,
                            "numfiles": 3,
                            "path": "S1234ABC/5/2",
                            "size": 302113
                        },
                        {
                            "number": 3,
                            "numfiles": 1,
                            "path": "S1234ABC/5/3",
                            "size": 23720011
                        }
                    ],
                    "studyDateTime": "Tue Mar 28 14:20:18 2017",
                    "studyNumber": 5,
                    "timePoint": "",
                    "visit": ""
                }
            ]
        }
    ]
}

{
    "clusterType": "sge",
    "clusterUser": "",
    "completeFiles": [
        "{analysisroot}/complete.txt"
    ],
    "createDate": "Mon Apr 6 14:26:18 2020",
    "dataCopyMethod": "nfs",
    "dataSpec": [
        {
            "associatonType": "nearestintime",
            "behDir": "",
            "behFormat": "behnone",
            "dataFormat": "nifti3d",
            "enabled": true,
            "gzip": true,
            "imageType": "",
            "level": "study",
            "location": "data",
            "modality": "MR",
            "numBOLDreps": 0,
            "numImagesCriteria": 0,
            "optional": true,
            "order": 1,
            "preserveSeries": false,
            "primaryProtocol": false,
            "protocol": "T1w",
            "seriesCriteria": "all",
            "usePhaseDir": false,
            "useSeries": false
        }
    ],
    "depDir": "root",
    "depLevel": "study",
    "depLinkType": "hardlink",
    "desc": "freesurfer for structural T1-weighted images",
    "dirStructure": "",
    "directory": "",
    "group": "",
    "groupType": "",
    "level": 1,
    "maxWallTime": 2880,
    "name": "freesurfer",
    "notes": "",
    "numConcurrentAnalysis": 30,
    "primaryScript": [
        {
            "command": "export FREESURFER_HOME=/opt/freesurfer",
            "desc": "The Freesurfer home directory (version) you want to use",
            "enabled": true,
            "logged": true,
            "order": 1,
            "workingdir": ""
        },
        {
            "command": "export FSFAST_HOME=/opt/freesurfer/fsfast",
            "desc": "Not sure if these next two are needed but keep them just in case",
            "enabled": true,
            "logged": true,
            "order": 2,
            "workingdir": ""
        },
        {
            "command": "export MNI_DIR=/opt/freesurfer/mni",
            "desc": "Not sure if these next two are needed but keep them just in case",
            "enabled": true,
            "logged": true,
            "order": 3,
            "workingdir": ""
        },
        {
            "command": "source $FREESURFER_HOME/SetUpFreeSurfer.sh",
            "desc": "MGH's shell script that sets up Freesurfer to run",
            "enabled": true,
            "logged": true,
            "order": 4,
            "workingdir": ""
        },
        {
            "command": "export SUBJECTS_DIR={analysisrootdir}",
            "desc": "Point to the subject directory you plan to use - all FS data will go there",
            "enabled": true,
            "logged": true,
            "order": 5,
            "workingdir": ""
        },
        {
            "command": "recon-all -notal-check -no-isrunning -all -subjid analysis",
            "desc": "Autorecon all {PROFILE}",
            "enabled": true,
            "logged": true,
            "order": 6,
            "workingdir": ""
        }
    ],
    "queue": "slow.*.q",
    "resultScript": "",
    "submitDelay": 0,
    "submitHost": "compute11",
    "tmpDir": "",
    "useProfile": true,
    "useTmpDir": false,
    "version": 1
}

#include "squirrel.h"

squirrel *sqrl = new squirrel();
sqrl->SetPackagePath("/path/to/data.sqrl");
if (sqrl->Read()) {
    cout << "Successfuly read squirrel package" << endl;
else
    cout << "Error reading squirrel package. Log [" << sqrl->GetLog() << "]" << endl;

/* print the entire package */
sqrl->Print();

/* access individual package meta-data */
cout << sqrl->name;

/* delete squirrel object */
delete sqrl;

/* iterate through the subjects */
QList<squirrelSubject> subjects = sqrl->GetSubjectList();
foreach (squirrelSubject subject, subjects) {
    cout <<"Found subject [" + subject.ID + "]");

    /* get studies */
    QList<squirrelStudy> studies = sqrl->GetStudyList(subject.GetObjectID());
    foreach (squirrelStudy study, studies) {
        n->Log(QString("Found study [%1]").arg(study.StudyNumber));

        /* get series */
        QList<squirrelSeries> serieses = sqrl->GetSeriesList(study.GetObjectID());
        foreach (squirrelSeries series, serieses) {
            n->Log(QString("Found series [%1]").arg(series.SeriesNumber));
            int numfiles = series.files.size();
        }
    }
}

/* get a subject by ID, the returned object is read-only */
qint64 subjectObjectID = FindSubject("12345");
squirrelSubject subject = GetSubject(subjectObjectID);
QString guid = subject.GUID;
subject.PrintDetails();

/* get a subject by SubjectUID (DICOM field) */
squirrelStudy study = GetStudy(FindSubjectByUID("08.03.21-17:51:10-STD-1.3.12.2.1107.5.3.7.20207"));
QString studyDesc = study.Description;
study.PrintDetails();

/* get study by subject ID, and study number */
squirrelStudy study = GetStudy(FindStudy("12345", 2));
QString studyEquipment = study.Equipment;
study.PrintDetails();

/* get series by seriesUID (DICOM field) */
squirrelSeries series = GetStudy(FindSeriesByUID("09.03.21-17:51:10-STD-1.3.12.2.1107.5.3.7.20207"));
QDateTime seriesDate = series.DateTime;
series.PrintDetails();

/* get series by subjectID 12345, study number 2, and series number 15 */
squirrelSeries series = GetStudy(FindSeries("12345", 2, 15));
QString seriesProtocol = series.Protocol;
series.PrintDetails();

/* get an analysis by subject ID 12345, study 2, and analysis 'freesurfer' */
squirrelAnalysis GetAnalysis(FindAnalysis("12345", 2, "freesurfer"));

/* get other objects by their names */
squirrelDataDictionary dataDictionary = GetDataDictionary(FindDataDictionary("MyDataDict"));
squirrelExperiment experiment = GetExperiment(FindExperiment("MyExperiment"));
squirrelGroupAnalysis groupAnalysis = GetGroupAnalysis(FindGroupAnalysis("MyGroupAnalysis"));
squirrelPipeline pipeline = GetPipeline(FindPipeline("MyPipeline"));

/* find a subject */

/* iterate by list to access copies of the objects(read only) */
foreach (squirrelExperiment exp, sqrl->experimentList) {
    cout << exp.experimentName << endl;
}
foreach (squirrelPipeline pipe, sqrl->pipelineList) {
    cout << pipe.pipelineName << endl;
}

/* iterate by index to change the original object (read/write) */
for (int i=0; i < sqrl->experimentList.size(); i++) {
    sqrl->experimentList[i].numFiles = 0;
}
for (int i=0; i < sqrl->pipelineList.size(); i++) {
    sqrl->pipelineList[i].numFiles = 0;
}

squirrel *sqrl = new squirrel();

/* set the package details */
sqrl->name = "LotsOfData";
sqrl->description = "My First squirrel package;
sqrl->datetime = QDateTime()::currentDateTime();
sqrl->subjectDirFormat = "orig";
sqrl->studyDirFormat = "orig";
sqrl->seriesDirFormat = "orig;
sqrl->dataFormat = "nifti";

/* create a subject */
squirrelSubject sqrlSubject;
sqrlSubject.ID = "123456";
sqrlSubject.alternateIDs = QString("Alt1, 023043").split(",");
sqrlSubject.GUID = "NDAR12345678";
sqrlSubject.dateOfBirth.fromString("2000-01-01", "yyyy-MM-dd");
sqrlSubject.sex = "O";
sqrlSubject.gender = "O";
sqrlSubject.ethnicity1 = subjectInfo->GetValue("ethnicity1");
sqrlSubject.ethnicity2 = subjectInfo->GetValue("ethnicity2");

/* add the subject. This subject has only demographics, there are no studies or  */
sqrl->addSubject(sqrlSubject);

/* see if we can find a subject by ID */
int subjIndex = sqrl->GetSubjectIndex("123456");
if (subjIndex >= 0) {

    /* build the study object */
    squirrelStudy sqrlStudy;
    sqrlStudy.number = 1;
    sqrlStudy.dateTime.fromString("2023-06-19 15:34:56", "yyyy-MM-dd hh:mm:ss");
    sqrlStudy.ageAtStudy = 34.5;
    sqrlStudy.height = 1.5; // meters
    sqrlStudy.weight = 75.9; // kg
    sqrlStudy.modality = "MR";
    sqrlStudy.description = "MJ and driving";
    sqrlStudy.studyUID = "";
    sqrlStudy.visitType = "FirstVisit";
    sqrlStudy.dayNumber = 1;
    sqrlStudy.timePoint = 1;
    sqrlStudy.equipment = "Siemens 3T Prisma;
    
    sqrl->subjectList[subjIndex].addStudy(sqrlStudy);
}
else {
    cout << "Unable to find subject by ID [123456]" << endl;
}

QString outdir = "/home/squirrel/thedata" /* output directory of the squirrel package */
QString zippath; /* the full filepath of the written zip file */

sqrl->write(outdir, zippath);++

./nidb: error while loading shared libraries: libsquirrel.so.1: cannot open shared object file: No such file or directory./nidb: error while loading shared libraries: libsquirrel.so.1: cannot open shared object file: No such file or directory

[nidb@ado2dev bin]$ ldd nidb
        linux-vdso.so.1 (0x00007ffd07fe4000)
        libSMTPEmail.so.1 => /lib/libSMTPEmail.so.1 (0x00007fdb4e2b0000)
        libsquirrel.so.1 => not found
        libgdcmMSFF.so.3.0 => /lib/libgdcmMSFF.so.3.0 (0x00007fdb4dd88000)
        libgdcmCommon.so.3.0 => /lib/libgdcmCommon.so.3.0 (0x00007fdb4db60000)
        libgdcmDICT.so.3.0 => /lib/libgdcmDICT.so.3.0 (0x00007fdb4d688000)
        libgdcmDSED.so.3.0 => /lib/libgdcmDSED.so.3.0 (0x00007fdb4d348000)

cd ~/squirrel/bin/squirrel
sudo cp -uv libsquirrel* /lib/

cd ~
git clone git@github.com:gbook/squirrel.git squirrel

cd ~/squirrel
git commit -am "Comments about the changes"
git push origin main

cd ~/squirrel
git pull origin main

sudo yum install swig python3-devel

swig -python gfg.i
gcc -c -fpic squirrel_wrap.c squirrel.cpp -I/usr/include/python3.6m

export FREESURFER_HOME=/opt/freesurfer-6.0     #  The Freesurfer home directory (version) you want to use
export FSFAST_HOME=/opt/freesurfer-6.0/fsfast     #  Not sure if these next two are needed but keep them just in case
export MNI_DIR=/opt/freesurfer-6.0/mni     #  Not sure if these next two are needed but keep them just in case
source $FREESURFER_HOME/SetUpFreeSurfer.sh     #  MGH's shell script that sets up Freesurfer to run
export SUBJECTS_DIR={analysisrootdir}     #  Point to the subject directory you plan to use - all FS data will go there
freesurfer > {analysisrootdir}/version.txt     # {NOLOG} get the freesurfer version
perl /opt/pipeline/ImportFreesurferData.pl {analysisrootdir}/data analysis     #  import data. the perl program allows importing of multiple T1s
recon-all -hippocampal-subfields-T1 -no-isrunning -all -notal-check -subjid analysis     #  Autorecon all {PROFILE}
if tail -n 1 {analysisrootdir}/analysis/scripts/recon-all-status.log | grep 'finished without error' ; then touch {analysisrootdir}/reconallsuccess.txt; fi     # {NOLOG} {NOCHECKIN}
recon-all -subjid analysis -qcache     #  do the qcache step {PROFILE}

#!/bin/sh
#$ -N freesurferUnified6
#$ -S /bin/bash
#$ -j y
#$ -o /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/pipeline/
#$ -V
#$ -u onrc
#$ -l h_rt=72:00:00
LD_LIBRARY_PATH=/opt/pipeline/nidb/; export LD_LIBRARY_PATH;
echo Hostname: `hostname`
echo Username: `whoami`

/opt/pipeline/nidb/nidb cluster -u pipelinecheckin -a 3151385 -s started -m 'Cluster processing started'
cd /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6;

/opt/pipeline/nidb/nidb cluster -u pipelinecheckin -a 3151385 -s processing -m 'processing step 1 of 10'
# The Freesurfer home directory (version) you want to use
echo Running export FREESURFER_HOME=/opt/freesurfer-6.0
export FREESURFER_HOME=/opt/freesurfer-6.0 >> /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/pipeline/Step1

/opt/pipeline/nidb/nidb cluster -u pipelinecheckin -a 3151385 -s processing -m 'processing step 2 of 10'
# Not sure if these next two are needed but keep them just in case
echo Running export FSFAST_HOME=/opt/freesurfer-6.0/fsfast
export FSFAST_HOME=/opt/freesurfer-6.0/fsfast >> /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/pipeline/Step2

/opt/pipeline/nidb/nidb cluster -u pipelinecheckin -a 3151385 -s processing -m 'processing step 3 of 10'
# Not sure if these next two are needed but keep them just in case
echo Running export MNI_DIR=/opt/freesurfer-6.0/mni
export MNI_DIR=/opt/freesurfer-6.0/mni >> /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/pipeline/Step3

/opt/pipeline/nidb/nidb cluster -u pipelinecheckin -a 3151385 -s processing -m 'processing step 4 of 10'
# MGH's shell script that sets up Freesurfer to run
echo Running source $FREESURFER_HOME/SetUpFreeSurfer.sh
source $FREESURFER_HOME/SetUpFreeSurfer.sh >> /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/pipeline/Step4

/opt/pipeline/nidb/nidb cluster -u pipelinecheckin -a 3151385 -s processing -m 'processing step 5 of 10'
# Point to the subject directory you plan to use - all FS data will go there
echo Running export SUBJECTS_DIR=/home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6
export SUBJECTS_DIR=/home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6 >> /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/pipeline/Step5

/opt/pipeline/nidb/nidb cluster -u pipelinecheckin -a 3151385 -s processing -m 'processing step 6 of 10'
# get the freesurfer version
echo Running freesurfer > /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/version.txt
freesurfer > /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/version.txt

/opt/pipeline/nidb/nidb cluster -u pipelinecheckin -a 3151385 -s processing -m 'processing step 7 of 10'
# import data. the perl program allows importing of multiple T1s
echo Running perl /opt/pipeline/ImportFreesurferData.pl /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/data analysis
perl /opt/pipeline/ImportFreesurferData.pl /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/data analysis >> /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/pipeline/Step7

/opt/pipeline/nidb/nidb cluster -u pipelinecheckin -a 3151385 -s processing -m 'processing step 8 of 10'
# Autorecon all {PROFILE}
echo Running recon-all -hippocampal-subfields-T1 -no-isrunning -all -notal-check -subjid analysis
/usr/bin/time -v recon-all -hippocampal-subfields-T1 -no-isrunning -all -notal-check -subjid analysis >> /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/pipeline/Step8
if tail -n 1 /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/analysis/scripts/recon-all-status.log | grep 'finished without error' ; then touch /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/reconallsuccess.txt; fi

/opt/pipeline/nidb/nidb cluster -u pipelinecheckin -a 3151385 -s processing -m 'processing step 10 of 10'
# do the qcache step {PROFILE}
echo Running recon-all -subjid analysis -qcache
/usr/bin/time -v recon-all -subjid analysis -qcache >> /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/pipeline/Step10

/opt/pipeline/nidb/nidb cluster -u pipelinecheckin -a 3151385 -s processing -m 'Processing result script'
# Running result script
echo Running perl /opt/pipeline/ParseFreesurferResults.pl -r /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6 -p /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/analysis/stats -a 3151385     #  dump results back into ado2 > /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/pipeline/stepResults.log 2>&1
perl /opt/pipeline/ParseFreesurferResults.pl -r /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6 -p /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/analysis/stats -a 3151385     #  dump results back into ado2 > /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6/pipeline/stepResults.log 2>&1
chmod -Rf 777 /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6
/opt/pipeline/nidb/nidb cluster -u pipelinecheckin -a 3151385 -s processing -m 'Updating analysis files'
/opt/pipeline/nidb/nidb cluster -u updateanalysis -a 3151385
/opt/pipeline/nidb/nidb cluster -u pipelinecheckin -a 3151385 -s processing -m 'Checking for completed files'
/opt/pipeline/nidb/nidb cluster -u checkcompleteanalysis -a 3151385
/opt/pipeline/nidb/nidb cluster -u pipelinecheckin -a 3151385 -s complete -m 'Cluster processing complete'
chmod -Rf 777 /home/pipeline/onrc/data/pipeline/S2907GCS/8/freesurferUnified6