{"id":"https://openalex.org/W7103656210","doi":"https://doi.org/10.5281/zenodo.17503171","title":"mhabbasiit/DTI: v1.0.0","display_name":"mhabbasiit/DTI: v1.0.0","publication_year":2025,"publication_date":"2025-11-01","ids":{"openalex":"https://openalex.org/W7103656210","doi":"https://doi.org/10.5281/zenodo.17503171"},"language":null,"primary_location":{"id":"doi:10.5281/zenodo.17503171","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.17503171","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":"article"},"type":"other","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.17503171","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":"middle","author":{"id":null,"display_name":"Chau Loo Kung, Gustavo","orcid":"https://orcid.org/0000-0002-3153-3868"},"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":"Chau Loo Kung, Gustavo","raw_affiliation_strings":["Stanford University"],"raw_orcid":"https://orcid.org/0000-0002-3153-3868","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":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"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/diffusion-mri","display_name":"Diffusion MRI","score":0.4797999858856201},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.4781999886035919},{"id":"https://openalex.org/keywords/distortion","display_name":"Distortion (music)","score":0.46399998664855957},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.43790000677108765},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.3939000070095062},{"id":"https://openalex.org/keywords/outlier","display_name":"Outlier","score":0.38609999418258667},{"id":"https://openalex.org/keywords/scanner","display_name":"Scanner","score":0.3537999987602234},{"id":"https://openalex.org/keywords/image-processing","display_name":"Image processing","score":0.3188999891281128}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7106000185012817},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5548999905586243},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.5457000136375427},{"id":"https://openalex.org/C149550507","wikidata":"https://www.wikidata.org/wiki/Q899360","display_name":"Diffusion MRI","level":3,"score":0.4797999858856201},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.4781999886035919},{"id":"https://openalex.org/C126780896","wikidata":"https://www.wikidata.org/wiki/Q899871","display_name":"Distortion (music)","level":4,"score":0.46399998664855957},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.43790000677108765},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.3939000070095062},{"id":"https://openalex.org/C79337645","wikidata":"https://www.wikidata.org/wiki/Q779824","display_name":"Outlier","level":2,"score":0.38609999418258667},{"id":"https://openalex.org/C2779751349","wikidata":"https://www.wikidata.org/wiki/Q1474480","display_name":"Scanner","level":2,"score":0.3537999987602234},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.3188999891281128},{"id":"https://openalex.org/C166704113","wikidata":"https://www.wikidata.org/wiki/Q861092","display_name":"Image registration","level":3,"score":0.3183000087738037},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3149999976158142},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.2980000078678131},{"id":"https://openalex.org/C55020928","wikidata":"https://www.wikidata.org/wiki/Q3813865","display_name":"Image quality","level":3,"score":0.29660001397132874},{"id":"https://openalex.org/C502989409","wikidata":"https://www.wikidata.org/wiki/Q11425","display_name":"Animation","level":2,"score":0.2955000102519989},{"id":"https://openalex.org/C103088060","wikidata":"https://www.wikidata.org/wiki/Q1062839","display_name":"Error detection and correction","level":2,"score":0.2770000100135803},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.27549999952316284},{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.271699994802475},{"id":"https://openalex.org/C106301342","wikidata":"https://www.wikidata.org/wiki/Q4117933","display_name":"Entropy (arrow of time)","level":2,"score":0.2687000036239624},{"id":"https://openalex.org/C131357438","wikidata":"https://www.wikidata.org/wiki/Q208598","display_name":"Eddy current","level":2,"score":0.26489999890327454},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.2558000087738037}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.5281/zenodo.17503171","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.17503171","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":"article"}],"best_oa_location":{"id":"doi:10.5281/zenodo.17503171","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.17503171","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":"article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Website":[0],"|":[1,3,5,7],"GitHub":[2],"YouTube":[4],"Wiki":[6],"QC":[8,182,261,268,578,643,688,788,794,811,814,850,857,888,894,953,1055,1223],"Sample":[9],"This":[10,216,492,649,807],"repository":[11],"contains":[12],"Python":[13],"code":[14,1097],"to":[15,111,230,240,318,324,326,345,371,378,396,406,423,451,672,691,717,753,978,1029,1050,1092,1132,1134,1140],"perform":[16],"preprocessing":[17,805,1010,1165],"of":[18,286,523,623,636,786,802,1174],"diffusion":[19,114,208,293,320,346,376,408,483,496,534,549,595,624,646,1008],"MRI":[20,209,294,497,535,625,1009],"(dMRI)":[21],"data.At":[22],"present,":[23],"the":[24,232,257,352,379,404,407,429,456,471,524,548,621,666,800,803,843,973,1007,1172],"only":[25],"distortion":[26],"correction":[27,75,153,179],"supported":[28],"is":[29,303,964,1079],"top-up":[30],"correction,":[31],"which":[32],"requires":[33],"an":[34],"additional":[35],"reversed":[36,166],"polarity":[37],"acquisition.":[38],"Prerequisites":[39],"FSL":[40,91,146,175,212,238,297,387],"ANTs":[41],"DIPY":[42,487,546],"Configuration":[43,59],"Paths":[44,910],"and":[45,73,108,132,142,154,160,171,221,227,247,254,290,322,361,410,412,431,442,447,503,518,539,566,572,598,654,665,712,747,798,813,819,869,874,911,948,1033,1046,1070,1095,1127],"file":[46,60,652,718,1071,1128,1150],"naming":[47],"are":[48,311,394,526,670,834,945,957,969,1083],"controlled":[49],"by":[50,139,1085],"config.py.":[51,751],"All":[52],"scripts":[53,1087],"work":[54],"on":[55,645,708,739,745],"a":[56,99,301,383,482,581,618,823,1148],"subject-by-subject":[57],"basis.":[58],"for":[61,271,366,416,463,529,620,676,736,880,985,1062],"neuroimaging":[62],"pipeline":[63,401,647],"Contains":[64],"settings":[65],"for:":[66],"Common":[67],"configurations":[68],"(paths,":[69],"logging,":[70],"etc.)":[71],"Topup":[72,84],"Eddy":[74,130],"Skull":[76,900],"stripping":[77,220],"DTI":[78,804,903,906],"fit":[79],"Registration":[80,370,690,876],"Processing":[81],"Steps":[82,157,235,332,419,531],"1.":[83],"Correction,":[85,134],"b0_correction.py":[86,1189],"Correct":[87,136],"susceptibility-induced":[88],"distortions":[89,137],"using":[90,145,211,296,339,351,382,455,470,486,545,658],"TOPUP":[92],"(Andersson":[93,148],"et":[94,489,990],"al.,":[95,490],"2003).This":[96],"step":[97,217,818,898],"estimates":[98],"field":[100],"map":[101,584],"from":[102,207,750,816,896,913],"images":[103,163,183,226,262,336,377,579,664,815,851,858,895],"with":[104,177,386,436,467,828,1053,1073,1153,1171],"opposite":[105],"phase-encoding":[106],"directions":[107],"applies":[109,403],"it":[110,680,836],"unwarp":[112],"distorted":[113],"volumes.":[115],"Reference:":[116,189,274,585,760,983],"Andersson,":[117,190],"J.L.R.,":[118,191],"Skare,":[119],"S.,":[120],"&":[121,149,192,590,613,777,882,935,1024],"Ashburner,":[122],"J.":[123],"(2003).":[124],"NeuroImage,":[125,196],"20(2),":[126],"870\u2013888.":[127],"https://pubmed.ncbi.nlm.nih.gov/14568458/":[128],"2.":[129],"Current":[131],"Motion":[133],"process_eddy.py":[135,1192],"caused":[138],"eddy":[140],"currents":[141],"subject":[143,1145,1155],"motion":[144],"EDDY":[147,176],"Sotiropoulos,":[150,193],"2016).Includes":[151],"slice-to-volume":[152,178],"outlier":[155],"replacement.":[156],"performed:":[158,236,333,420,532],"Load":[159,533],"merge":[161],"diffusion-weighted":[162],"(AP/PA":[164],"or":[165],"polarity)":[167],"Prepare":[168,1144],"acquisition":[169],"parameters":[170],"B0":[172,314,335,422,433,444,848],"indices":[173],"Run":[174,1164],"(optional)":[180],"Generate":[181,244,577],"comparing":[184],"original":[185],"vs":[186],"corrected":[187,847],"volumes":[188,347,409],"S.N.":[194],"(2016).":[195],"125,":[197],"1063\u20131078.":[198],"https://pubmed.ncbi.nlm.nih.gov/26481672/":[199],"3.":[200],"Brain":[201,279,859],"Extraction,":[202],"brain_extraction.py":[203,1195],"Removes":[204],"non-brain":[205,242],"tissue":[206,243],"data":[210,498,1217],"BET":[213,239],"(Smith,":[214],"2002).":[215],"performs":[218],"skull":[219],"generates":[222],"quality":[223,657,1064],"control":[224],"(QC)":[225],"summary":[228,269],"files":[229,1035],"validate":[231,255],"extracted":[233],"brain.":[234],"Apply":[237,343,445],"remove":[241],"brain":[245,251,540,865],"mask":[246,466,541,862],"masked":[248],"output":[249],"Compute":[250],"volume":[252,866],"(ml)":[253],"against":[256],"expected":[258],"range":[259],"Create":[260,1147],"(raw,":[263],"brain-extracted,":[264],"raw+mask,":[265],"differences)":[266],"Write":[267],"(CSV)":[270],"downstream":[272,367,417,677],"review":[273],"Smith,":[275],"S.M.":[276],"(2002).":[277],"Human":[278],"Mapping,":[280],"17(3),":[281],"143\u2013155.":[282],"https://pubmed.ncbi.nlm.nih.gov/12391568/":[283],"4.":[284],"Merging":[285],"Acquisitions,":[287],"reg_within_fsl.py":[288,1198],"Aligns":[289],"merges":[291],"multiple":[292,307],"runs":[295,338],"FLIRT":[298,340,388],"in":[299,628,742,842,959,980,1130,1176,1221],"case":[300],"session":[302,939,1018],"broken":[304],"down":[305],"into":[306,822],"acquisitions.":[308,1142],"Rigid":[309],"transformations":[310,459,474],"estimated":[312],"between":[313,337,662],"reference":[315],"images,":[316],"applied":[317],"corresponding":[319],"volumes,":[321,359,856],"propagated":[323],"b-vectors":[325,350,393,454],"ensure":[327,1051,1093],"orientation":[328,398],"consistency":[329,464,1094],"across":[330,1006],"runs.":[331],"Register":[334,421,465],"rigid-body":[341],"transform":[342,1034],"transforms":[344,405,450],"(DWI)":[348],"Rotate":[349,453],"computed":[353,458,473],"transformation":[354],"matrix":[355,430],"Merge":[356],"registered":[357,432,443],"DWI":[358,452],"b-vectors,":[360,538],"b-values":[362,461],"Save":[363,562],"combined":[364],"outputs":[365,415,504,801,1213,1215],"processing":[368],"5.":[369],"MNI":[372,424,667,692,699,883],"Space,":[373],"run_reg_mni.py":[374,1201],"Registers":[375],"MNI152":[380],"template":[381,700],"two-step":[384],"approach":[385],"(rigid":[389,693],"+":[390,694,719,864],"affine).":[391],"Corresponding":[392],"rotated":[395],"preserve":[397],"consistency.":[399],"The":[400],"also":[402,527,837],"masks,":[411],"prepares":[413],"final":[414],"analysis.":[418],"(rigid,":[425],"6":[426],"DOF),":[427,439],"save":[428,440],"Refine":[434],"B0\u2192MNI":[435],"affine":[437,449],"(12":[438],"matrix,":[441],"rigid":[446],"then":[448],"previously":[457,472],"Copy":[460],"(bval_final.bval)":[462],"nearest-neighbour":[468],"interpolation":[469],"6.":[475],"Diffusion":[476],"Tensor":[477],"Model":[478],"Fitting,":[479],"run_dtifit_dipy.py":[480,1204],"Fits":[481],"tensor":[484,525,550,554,564,596],"model":[485,551],"(Garyfallidis":[488],"2014).":[491],"script":[493,650,808],"takes":[494],"preprocessed":[495],"(DWI,":[499],"bvec,":[500],"bval,":[501],"mask)":[502],"standard":[505],"DTI-derived":[506,563],"measures":[507],"including":[508],"fractional":[509],"anisotropy":[510],"(FA),":[511],"mean":[512],"diffusivity":[513,516,520],"(MD),":[514],"radial":[515],"(RD),":[517],"axial":[519],"(AD).":[521],"Eigenvectors":[522],"saved":[528],"visualization.":[530],"data,":[536],"b-values,":[537],"Construct":[542],"gradient":[543],"table":[544],"Fit":[547],"voxel-wise":[552],"Extract":[553],"components":[555,565],"(Dxx,":[556],"Dxy,":[557],"Dxz,":[558],"Dyy,":[559],"Dyz,":[560],"Dzz)":[561],"maps:":[567,907],"FA,":[568],"MD,":[569],"RD,":[570],"AD,":[571],"eigenvectors":[573],"(V1,":[574],"V2,":[575],"V3)":[576],"showing":[580],"color":[582],"FA":[583,868],"Basser,":[586],"P.J.,":[587],"Mattiello,":[588],"J.,":[589],"LeBihan,":[591],"D.":[592],"(1994).":[593],"MR":[594],"spectroscopy":[597],"imaging.":[599],"Biophysical":[600],"Journal,":[601],"66(1),":[602],"259\u2013267.":[603],"https://pubmed.ncbi.nlm.nih.gov/8130344/":[604],"Garyfallidis,":[605],"E.,":[606],"Brett,":[607],"M.,":[608],"Correia,":[609],"M.M.,":[610],"Williams,":[611],"G.B.,":[612],"Nimmo-Smith,":[614],"I.":[615],"(2014).":[616],"DIPY,":[617],"library":[619],"analysis":[622],"data.":[626],"Frontiers":[627],"Neuroinformatics,":[629],"8,":[630],"8.":[631,784],"https://pmc.ncbi.nlm.nih.gov/articles/PMC3931231/":[632],"7.":[633],"Quality":[634],"Control":[635],"Final":[637],"Outputs,":[638],"run_final_qc.py":[639,1207],"Performs":[640],"automated,":[641,792],"session-aware":[642],"checks":[644],"outputs.":[648],"validates":[651],"existence":[653,683],"assesses":[655],"registration":[656,702,756],"overlap":[659,986],"metrics":[660],"(Dice)":[661],"warped":[663],"template.":[668],"Results":[669],"written":[671],"per-session":[673,713],"CSV":[674],"reports":[675,795],"review.":[678],"What":[679],"checks:":[681],"File":[682,1022],"validation":[684],"(key":[685],"outputs,":[686],"matrices,":[687],"images)":[689],"affine),":[695],"Dice":[696,707,740,878,984],"coefficient":[697],"vs.":[698,846,854],"Within-session":[701],"(if":[703],"NUM_SCANS_PER_SESSION":[704,729,1138],">":[705,730],"1),":[706],"b0-to-b0":[709],"Session":[710,1014],"discovery":[711],"reporting":[714],"Structured":[715],"logging":[716,1072],"console":[720,1069],"Outputs":[721],"(CSV":[722],"per":[723,1157],"subject/session):":[724],"QC/file_existance.csv":[725],"QC/within_subject_registraction_qc.csv":[726],"(only":[727],"if":[728,938,1076],"1)":[731,1122],"QC/mni_registraction_qc.csv":[732],"Notes:":[733],"Uses":[734,972],"thresholds":[735],"PASS/WARNING":[737],"based":[738],"(configurable":[741],"code).":[743],"Relies":[744],"TEMPLATE_PATH":[746],"derivative":[748],"folders":[749,1019],"Designed":[752],"run":[754,979],"after":[755],"steps":[757,884],"have":[758],"completed.":[759],"Zou,":[761,988],"K.H.,":[762,989],"Warfield,":[763],"S.K.,":[764],"Bharatha,":[765],"A.,":[766],"Tempany,":[767],"C.M.,":[768],"Kaus,":[769],"M.R.,":[770],"Haker,":[771],"S.J.,":[772],"Wells,":[773],"W.M.,":[774],"Jolesz,":[775],"F.A.,":[776],"Kikinis,":[778],"R.":[779],"(2004),":[780],"11(2),":[781,995],"178\u2013189.":[782,996],"https://pubmed.ncbi.nlm.nih.gov/14974593/":[783,997],"Generation":[785],"HTML":[787,825],"Reports,":[789],"dti_qc.py":[790,1210],"Generates":[791],"subject-level":[793],"that":[796],"summarize":[797],"visualize":[799],"pipeline.":[806,1011],"reads":[809],"existing":[810],"CSVs":[812,889],"each":[817,897],"compiles":[820],"them":[821],"clickable":[824],"report":[826],"along":[827],"CSV/JSON":[829],"summaries.":[830],"If":[831,962],"FA/MD":[832],"maps":[833],"available,":[835,966],"computes":[838],"basic":[839],"statistics.":[840],"Summarized":[841],"report:":[844],"Raw":[845],"(Topup),":[849],"(before/after)":[852],"Eddy-corrected":[853],"uncorrected":[855],"extraction":[860],"evaluation,":[861],"overlays":[863],"(mL)":[867],"color-FA":[870],"maps,":[871],"quick-look":[872],"thumbnails":[873],"stats":[875],"metrics,":[877],"coefficients":[879],"within-session":[881],"Inputs":[885],"(read-only):":[886],"Existing":[887],"(e.g.,":[890,915,942,955,1020,1088],"file_existance.csv,":[891],"within_subject_registraction_qc.csv,":[892],"mni_registraction_qc.csv)":[893],"(Topup,":[899],"stripping,":[901],"Eddy,":[902],"fit)":[904],"Optional":[905],"dipy_fa.nii.gz,":[908],"dipy_md.nii.gz":[909],"flags":[912],"config.py":[914,1131],"OUTPUT_DIR,":[916],"NUM_SCANS_PER_SESSION)":[917],"Outputs:":[918],"Per-subject":[919,922,925],"JSON:":[920],"<QC>/<subject_id>/<subject_id>_qc_results.json":[921],"CSV:":[923,929],"<QC>/<subject_id>/<subject_id>_qc_summary.csv":[924],"HTML:":[926,932],"<QC>/<subject_id>/<subject_id>_report.html":[927],"Aggregated":[928,931],"<QC>/all_subjects_summary.csv":[930],"<QC>/DTI_QC_Summary.html":[933],"Behavior":[934],"notes:":[936],"Session-aware:":[937],"directories":[940],"exist":[941],"YYYY-MM-DD),":[943],"they":[944],"automatically":[946,1016],"detected":[947],"linked.":[949],"Read-only":[950],"summarization;":[951],"heavy":[952],"computations":[954],"Dice)":[956],"performed":[958],"earlier":[960],"scripts.":[961],"nilearn":[963],"not":[965],"visualization":[967],"sections":[968],"safely":[970],"skipped.":[971],"non-interactive":[974],"Matplotlib":[975],"backend":[976],"(Agg)":[977],"headless":[981],"environments.":[982],"validation:":[987],"al.":[991],"(2004).":[992],"Academic":[993],"Radiology,":[994],"9.":[998],"Utility":[999],"Functions,":[1000],"utilities.py":[1001],"Provides":[1002],"supporting":[1003],"functions":[1004],"used":[1005],"Key":[1012],"functionalities:":[1013],"Detection,":[1015],"identifies":[1017],"YYYY-MM-DD).":[1021],"Search":[1023],"Matching,":[1025],"robust":[1026],"pattern":[1027],"matching":[1028],"locate":[1030],"NIfTI,":[1031],"bvec/bval,":[1032],"even":[1036],"when":[1037],"filenames":[1038],"differ":[1039],"slightly.":[1040],"NIfTI":[1041],"Handling,":[1042],"inspects":[1043],"image":[1044],"dimensions":[1045,1049],"trims":[1047],"odd":[1048],"compatibility":[1052],"FSL/ANTs.":[1054],"Image":[1056],"Generation,":[1057],"creates":[1058],"slice-wise":[1059],"PNG":[1060],"snapshots":[1061],"quick":[1063],"checks.":[1065],"Logging":[1066],"Utilities,":[1067],"initializes":[1068],"safe":[1074],"fallbacks":[1075],"write":[1077],"access":[1078],"restricted.":[1080],"These":[1081],"utilities":[1082],"imported":[1084],"other":[1086],"b0_correction.py,":[1089],"process_eddy.py,":[1090],"brain_extraction.py)":[1091],"avoid":[1096],"duplication.":[1098],"Authors:":[1099],"Mohammad":[1100],"H":[1101],"Abbasi":[1102],"(mabbasi":[1103],"[at]":[1104,1109],"stanford.edu)":[1105,1110],"Gustavo":[1106],"Chau":[1107],"(gchau":[1108],"Stanford":[1111],"University,":[1112],"STAI":[1113],"Lab":[1114],"(https://stai.stanford.edu)":[1115],"Created:":[1116],"2025":[1117],"Version:":[1118],"1.0.0":[1119],"Quick":[1120],"Start":[1121],"Edit":[1123],"configuration":[1124],"Update":[1125],"paths":[1126],"patterns":[1129],"point":[1133],"your":[1135,1141,1177],"dataset.":[1136],"Set":[1137],"according":[1139],"2)":[1143],"list":[1146],"text":[1149],"named":[1151],"subject_list.txt":[1152],"one":[1154],"ID":[1156],"line,":[1158],"e.g.:":[1159],"sub-0001":[1160],"sub-0002":[1161],"sub-0003":[1162],"3)":[1163],"Submit":[1166],"array":[1167],"jobs":[1168],"(replace":[1169],"N":[1170],"number":[1173],"subjects":[1175],"list)":[1178],"sbatch":[1179],"--array=1-N":[1180],"run_b0_correction.sh":[1181],"Pipeline":[1182,1184],"order":[1183,1185],"(per":[1186],"subject)":[1187],"python":[1188,1191,1194,1197,1200,1203,1206,1209],"<subject_id>":[1190,1193,1196,1199,1202,1205,1208,1211],"Check":[1212,1214],"Preprocessed":[1216],"\u2192":[1218,1225],"<OUTPUT_DIR>":[1219],"(set":[1220],"config.py)":[1222],"results":[1224],"<OUTPUT_DIR>/QC/":[1226]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-11-02T00:00:00"}