{"id":"https://openalex.org/W7103654534","doi":"https://doi.org/10.5281/zenodo.17503175","title":"mhabbasiit/sMRI: v1.0.0","display_name":"mhabbasiit/sMRI: v1.0.0","publication_year":2025,"publication_date":"2025-11-01","ids":{"openalex":"https://openalex.org/W7103654534","doi":"https://doi.org/10.5281/zenodo.17503175"},"language":null,"primary_location":{"id":"doi:10.5281/zenodo.17503175","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.17503175","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},"type":"software","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.17503175","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Abbasi, Mohammad H.","orcid":"https://orcid.org/0000-0002-3737-1652"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Abbasi, Mohammad H.","raw_affiliation_strings":["Stanford University"],"raw_orcid":"https://orcid.org/0000-0002-3737-1652","affiliations":[{"raw_affiliation_string":"Stanford University","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":null,"display_name":"Adeli, Ehsan","orcid":"https://orcid.org/0000-0002-0579-7763"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adeli, Ehsan","raw_affiliation_strings":["Stanford University"],"raw_orcid":"https://orcid.org/0000-0002-0579-7763","affiliations":[{"raw_affiliation_string":"Stanford University","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":true,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7087000012397766},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.705299973487854},{"id":"https://openalex.org/keywords/cache","display_name":"Cache","score":0.40369999408721924},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.34709998965263367},{"id":"https://openalex.org/keywords/overlay","display_name":"Overlay","score":0.322299987077713},{"id":"https://openalex.org/keywords/rendering","display_name":"Rendering (computer graphics)","score":0.29789999127388}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7329999804496765},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7087000012397766},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.705299973487854},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.4253000020980835},{"id":"https://openalex.org/C115537543","wikidata":"https://www.wikidata.org/wiki/Q165596","display_name":"Cache","level":2,"score":0.40369999408721924},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.34709998965263367},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3467999994754791},{"id":"https://openalex.org/C136085584","wikidata":"https://www.wikidata.org/wiki/Q910289","display_name":"Overlay","level":2,"score":0.322299987077713},{"id":"https://openalex.org/C205711294","wikidata":"https://www.wikidata.org/wiki/Q176953","display_name":"Rendering (computer graphics)","level":2,"score":0.29789999127388},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2937000095844269},{"id":"https://openalex.org/C2780940931","wikidata":"https://www.wikidata.org/wiki/Q174989","display_name":"File system","level":2,"score":0.2888999879360199},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.28189998865127563},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.26429998874664307},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2639999985694885},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.262800008058548},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.2549999952316284}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.5281/zenodo.17503175","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.17503175","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Software"}],"best_oa_location":{"id":"doi:10.5281/zenodo.17503175","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.17503175","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Structural":[0],"MRI":[1,687],"Processing":[2,50,197,649,678,710],"PipelineWebsite":[3],"|":[4,6,8,10,622],"GitHub":[5],"YouTube":[7],"Wiki":[9],"QC":[11,30,179,224,446,451],"Sample":[12],"A":[13,680,712],"lightweight,":[14,681,713],"end\u2011to\u2011end":[15],"pipeline":[16,662],"for":[17,98,144,309,462,684,716],"brain":[18,250,454,549,718],"extraction,":[19],"registration":[20,406,484,555],"to":[21,267,275,287,338,422,571,627,654],"MNI,":[22,339],"post\u2011processing":[23],"(N4":[24],"+":[25,28],"masked":[26,346],"Z\u2011score":[27],"cropping),":[29],"visualization,":[31],"and":[32,124,223,232,253,352,448,486,493,500,636,689,704,721],"CSV":[33,190,452,480,599],"metadata":[34,565,600],"generation.":[35],"The":[36,134,208],"structure":[37,166],"of":[38,289],"this":[39,218,661],"README":[40],"mirrors":[41],"the":[42,284,290,350,404,628],"DTI":[43],"project":[44],"style:":[45],"Prerequisites":[46,60],"\u2192":[47,49,53,56,58,212,214,270,361,575,582,588,601],"Configuration":[48,122],"Steps":[51,198,357],"(numbered)":[52],"Quick":[54,510],"Start":[55,511],"Outputs/QC":[57],"Authors/Version.":[59],"Python":[61,64],"\u2265":[62],"3.8":[63],"packages:":[65],"numpy,":[66],"nibabel,":[67],"SimpleITK,":[68,634],"matplotlib,":[69],"tqdm,":[70],"templateflow,":[71],"pandas":[72,121,534],"SynthStrip":[73],"via":[74,230],"one":[75],"of:":[76],"Singularity":[77,211],"image:":[78,82],"freesurfer/synthstrip:latest":[79,83],"(recommended)":[80],"Docker":[81,213],"FreeSurfer":[84,215],"installation":[85],"with":[86,150,249,363,453,496],"mri_synthstrip":[87],"in":[88,159,239,318,663],"$FREESURFER_HOME/bin":[89],"(Optional)":[90,96],"TemplateFlow":[91],"cache":[92],"(auto\u2011downloads":[93],"MNI152NLin2009cAsym":[94,276],"template)":[95],"conda":[97,104,110,517,523],"environment":[99,516],"management":[100],"Example":[101],"env":[102],"setup":[103],"create":[105,515,518],"-y":[106,519],"-n":[107,520],"smri":[108,112,521,525],"python=3.10":[109,522],"activate":[111,524],"pip":[113,526],"install":[114,527],"numpy":[115,528],"nibabel":[116,529],"SimpleITK":[117,279,530],"matplotlib":[118,531],"tqdm":[119,532],"templateflow":[120,533],"Paths":[123],"behavior":[125],"are":[126,136,142],"controlled":[127],"by":[128,131],"config.py":[129,155,540,543],"(shared":[130],"all":[132,260],"scripts).":[133],"scripts":[135],"primarily":[137],"config\u2011driven;":[138],"minimal":[139],"CLI":[140,255,326,429,507],"flags":[141],"provided":[143],"convenience.":[145],"Privacy\u2011safe":[146],"release:":[147],"publish":[148],"config.example.py":[149,539],"placeholders;":[151],"keep":[152],"your":[153,664],"real":[154],"untracked.":[156],"Key":[157],"items":[158],"config.py:":[160],"Paths:":[161],"INPUT_DIR,":[162],"OUTPUT_DIR,":[163],"STAGE_ROOTS":[164],"Unified":[165],"pattern:":[167],"STRUCTURE":[168,231],"=":[169,374,700,708,725,728,736,739,742],"\"{root}/{subject}/{session}/anat\"":[170],"Patterns:":[171],"SKULLSTRIP_T1_FILE_PATTERN,":[172],"SKULLSTRIP_T2_FILE_PATTERN":[173],"Processing:":[174],"MODALITIES,":[175],"SUBJECTS,":[176],"SESSIONS,":[177],"FORCE_REPROCESSING":[178],"thresholds,":[180],"logging,":[181],"CPU":[182],"threads":[183],"Registration:":[184],"MNI_TEMPLATE_VERSION,":[185],"MNI_TEMPLATE_RESOLUTION":[186],"Post\u2011process:":[187],"POSTPROCESS_APPLY_N4,":[188],"POSTPROCESS_CROP_MARGIN":[189],"metadata:":[191],"output":[192],"dir,":[193],"columns,":[194],"demographics":[195,498],"encoders":[196],"1)":[199,536],"Brain":[200],"Extraction,":[201],"skullstrip.py":[202,257,262,443,552],"Removes":[203],"non\u2011brain":[204],"tissue":[205],"using":[206,278,365],"SynthStrip.":[207],"script":[209],"tries":[210],"binary":[216],"(in":[217],"order).":[219],"Generates":[220],"brain,":[221,351],"mask,":[222],"images.":[225],"Inputs":[226],"NIfTI":[227],"files":[228],"discovered":[229],"patterns:":[233],"*acq-MPRAGE_T1w.nii.gz":[234],"*acq-CUBE_T2w.nii.gz":[235],"Outputs":[236,315,400,469,504,569],"(per":[237,316,401],"subject/session":[238,317],"STAGE_ROOTS[\"skullstrip\"])":[240],"*_brain.nii.gz,":[241],"*_brain_mask.nii.gz":[242],"*_desc-qc.png":[243],"overlay":[244],"montage":[245,399],"Global":[246],"CSV:":[247],"QC/qc_summary.csv":[248,470,580],"volume":[251],"(ml)":[252],"PASS/FAIL":[254],"python":[256,261,327,329,430,432,508,551,556,561,567],"#":[258,512,535,541,547,553,558,563],"process":[259],"--subject":[263,331,434],"sub-ON12345":[264,332,435],"2)":[265,548],"Registration":[266,581],"MNI":[268,362,490],"(Rigid":[269],"Affine),":[271],"reg.py":[272,328,330,557],"Registers":[273],"T1w":[274],"(1mm)":[277],"(Mattes":[280],"MI;":[281],"multi\u2011resolution).":[282],"Applies":[283],"same":[285,291,405,589],"transforms":[286,314],"T2w":[288],"session.":[292],"Method":[293],"Rigid:":[294],"Euler3D,":[295],"shrink":[296,301],"[4,2,1],":[297],"linear":[298,303],"Affine:":[299],"12\u2011DOF,":[300],"[2,1],":[302],"Final":[304],"resampling:":[305],"composite":[306,366],"transform":[307,367],"(rigid+affine)":[308,368],"single":[310],"interpolation":[311],"Saves":[312],"*.mat":[313],"STAGE_ROOTS[\"registration\"])":[319],"*_mni_rigid_warped.nii.gz":[320],"(QC/ref)":[321],"*_mni_warped.nii.gz":[322],"(final)":[323],"other/*_rigid.mat,":[324,585],"other/*_affine.mat":[325,586],"3)":[333,554],"Post\u2011processing,":[334],"postprocess_mni_mask_zscore_crop.py":[335,431,433,562],"Warp":[336,358],"masks":[337,360],"run":[340],"N4":[341,369,411],"bias":[342,370],"correction":[343,371],"(optional),":[344],"compute":[345],"Z\u2011score,":[347,492],"crop":[348],"around":[349],"save":[353],"a":[354,449],"multi\u2011slice":[355,397],"visualization.":[356],"native":[359],"nearest\u2011neighbor":[364],"(if":[372,410],"POSTPROCESS_APPLY_N4":[373],"True)":[375],"Masked":[376],"Z\u2011score:":[377],"\u03bc/\u03c3":[378],"computed":[379],"within":[380],"mask;":[381],"background":[382],"kept":[383],"at":[384],"0":[385],"Crop:":[386],"tight":[387],"bounding":[388],"box":[389],"(+":[390],"POSTPROCESS_CROP_MARGIN),":[391],"affine":[392],"updated":[393],"(qform/sform":[394],"set)":[395],"Save":[396],"PNG":[398],"subject/session;":[402],"under":[403,591],"anat/)":[407],"T1w_mni_mask.nii.gz":[408],"T1w_mni_warped_n4.nii.gz":[409],"enabled)":[412],"T1w_mni_zscore_fixed.nii.gz":[413],"T1w_mni_zscore_fixed_cropped.nii.gz":[414],"multislice_visualization_<subj>.png":[415,595],"(T2":[416],"equivalents":[417],"when":[418],"available;":[419],"falls":[420],"back":[421],"T1":[423],"mask":[424,427],"if":[425],"T2":[426,597],"missing)":[428],"4)":[436,559],"Quality":[437],"Control":[438],"&":[439,644,673],"Reports,":[440],"skullstrip.py,":[441],"structural_qc.py":[442,456],"writes":[444],"per\u2011subject":[445],"montages":[447],"global":[450,579],"volume.":[455],"(optional":[457],"helpers)":[458],"can":[459],"be":[460],"used":[461],"extended":[463],"validations":[464],"(e.g.,":[465],"Dice":[466],"vs":[467],"reference).":[468],"(columns:":[471],"input_file,":[472],"output_file,":[473],"modality,":[474],"qc_status,":[475],"brain_volume_ml,":[476],"qc_image_path,":[477],"error_message)":[478],"5)":[479,564],"Metadata,":[481],"generate_csv_metadata.py":[482,509,568],"Scans":[483],"outputs":[485],"builds":[487],"CSVs":[488],"listing":[489],"warped,":[491],"cropped":[494],"paths,":[495,545],"optional":[497],"(participants.tsv)":[499],"encodings":[501],"(sex,":[502],"handedness).":[503],"metadata/T1_metadata.csv":[505],"metadata/T2_metadata.csv":[506],"0)":[513],"(optional)":[514],"configure":[537],"cp":[538],"edit":[542],"(private":[544],"thresholds)":[546],"extraction":[550],"post-process":[560],"tables":[566],"(Where":[570],"Find":[572],"Things)":[573],"Skullstrip":[574],"STAGE_ROOTS[\"skullstrip\"]*_brain.nii.gz,":[576],"*_brain_mask.nii.gz,":[577],"*_desc-qc.png,":[578],"STAGE_ROOTS[\"registration\"]*_mni_rigid_warped.nii.gz,":[583],"*_mni_warped.nii.gz,":[584],"Post\u2011process":[587],"anat/":[590],"registrationT1w_mni_mask.nii.gz,":[592],"T1w_mni_zscore_fixed.nii.gz,":[593],"T1w_mni_zscore_fixed_cropped.nii.gz,":[594],"(and":[596],"analogs)":[598],"CSV_METADATA_DIRT1_metadata.csv,":[602],"T2_metadata.csv":[603],"Authors":[604],"/":[605],"Version":[606],"Author:":[607],"Mohammad":[608],"H.":[609],"Abbasi":[610,703],"(mabbasi":[611],"[at]":[612],"stanford.edu)":[613],"Lab:":[614],"Stanford":[615,695,733],"University,":[616],"STAI":[617],"Lab":[618],"(https://stai.stanford.edu)":[619],"Created:":[620],"2025":[621],"Version:":[623],"1.0.0":[624],"Acknowledgements":[625],"Thanks":[626],"open\u2011source":[629],"neuroimaging":[630],"community":[631],"(FreeSurfer,":[632],"TemplateFlow,":[633],"nibabel)":[635],"dataset":[637],"providers.":[638],"Citation":[639],"(short":[640],"version)":[641],"Abbasi,":[642,671],"M.H.,":[643,672],"Adeli,":[645,674],"E.":[646,675],"(2025).":[647,676],"sMRI":[648,677],"Pipeline.":[650],"Zenodo.DOI:":[651],"10.5281/zenodo.17503175":[652],"How":[653],"Cite":[655],"This":[656],"Work":[657],"If":[658],"you":[659],"use":[660],"research,":[665],"please":[666],"cite":[667],"it":[668],"as":[669],"follows:":[670],"Pipeline:":[679,711],"end-to-end":[682,714],"framework":[683],"BIDS-compatible":[685],"structural":[686,717],"preprocessing":[688,720],"quality":[690,722],"control.Stanford":[691],"Translational":[692,730],"AI":[693,731],"Lab,":[694,732],"University.":[696],"Zenodo.https://doi.org/10.5281/zenodo.17503175":[697],"@software{abbasi2025smri,":[698],"author":[699],"{Mohammad":[701],"Hassan":[702],"Ehsan":[705],"Adeli},":[706],"title":[707],"{{sMRI}":[709],"workflow":[715],"{MRI}":[719],"control},":[723],"year":[724],"{2025},":[726],"institution":[727],"{Stanford":[729],"University},":[734],"publisher":[735],"{Zenodo},":[737],"doi":[738],"{10.5281/zenodo.17503175},":[740],"url":[741],"{https://doi.org/10.5281/zenodo.17503175}":[743],"}":[744]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2025-11-02T00:00:00"}