Detailed Steps for DTI Data Processing.docx

Detailed Steps for DTI Data Processing.docx

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DetailedStepsforDTIDataProcessing

OriginalDataLocation:

192.168.69.5:

/mnt/data1/Orig_XieHe_Epilepsy/XieHe-DTI-Dicom

PartI.DataPreparation

1.Copytheoriginaldatato/usr/test/XieHe-DTI-Dicom

2.DataConversion:

changethedirectoryto/usr/test/XieHe-DTI-Dicom,thenrundcm2nii‘/usr/test/XieHe-DTI-Dicom’.

wehavemanysubfoldersholdingDICOMfilesin/usr/test/XieHe-DTI-Dicomnamedbythesubjects'name.Rundcm2nii'/usr/test/XieHe-DTI-Dicom'intheterminal,youwillconverttheDICOMfileslocatedinthesubfoldersto.niifiles,andeachofthenewcreated.niifilesarelocatedinthecorrespondingsubfolder.Thisissimilartorundcm2nii/usr/test/XieHe-DTI-Dicom/subjname/usr/test/XieHe-DTI-Dicom/subjnameforeverysubjects.

3.Copythenewcreated.niifilesto/usr/test/data

（1）changdirectoryto/usr/test

（2）RunsudocpXieHe-DTI-Dicom/*/*.nii/usr/test/data

4.Removetheunfavorablefilesin/usr/test/data

5.Renameallthefiles,discardalltheunnecessarycodes

Here,weneedasoftwarenamedThunar,andsomesimpleregularexpression.Hereisaquicktutorial.

PartII.Preprocessing：

createFAimagesfromdiffusionstudydata

1.EddyCurrentCorrection

（1）Stayindirectory/usr/test//data.

（2）Acommandlineutilityiseddy_correct<4dinput><4doutput>

ForThisstudy,‘4dinput’isthe.niifilename.andIdefine‘4doutput’as‘E_’+’theoriginalfilename’.reference_nois0.So,wegetaexampleaseddy_correctCHENGYE.niiE_CHENGYE.nii0.Ittakes~30min.ObviouslyIcannotwaitandtypeacommandevery30min.HereIusescriptstosavethetrouble.

（3）Creatafilenamededdycorrect.sh:

sudogediteddycorrect.sh.（editwithEmEditorandExcelinthelocalcomputer,andthencopythecodestotheremotecomputer）

（4）Applyexecutepermissionstoeddycorrect.sh:

sudochmod+Xeddycorrect.shorsudochmod–R777eddycorrect.sh.

（5）Executebulkeddycorrect:

./eddycorrect.sh.

2.Diffusiondatareconstructionandfibertracking（youcanskipthissectionifyouwantrunonlyTBSS）

WeneedezDICOMorMatlabtocheckDICOMinfo,DiffusionToolkitandTrackVistodothedetailedworks.

（1）DownloadandinstallezDICOM,Matlab,DiffusionToolkitandTrackVisinaWinXpcomputer（Localcomputer）.

（2）ChecktheDICOMinformationfordatareconstruction,especiallytheScannertypeandImageorientation.Hereisatutorial.Forthisstudy,Scanner=GE,Imageorientation=（1,0,0）,（0,1,0）.

（3）CopytheE_*.nii.gz（Imagedataaftereddycurrentcorrection）andthecorresponding.BVALand.BVECfiletolocalcomputer（usingsecureshellclient）.

（4）LaunchDiffusionToolKit

1）SettheImagingmodeltoDTIandmarkthecheckboxofReconstruction.

2）settheRawdatafilespathpointingtotheE_*.nii.gzfile.

3）EdittheGradienttable:

Openthecorresponding.bvecfile,delectethefirstlineofit（typically,thefirstlineis‘000’）andcopytheremaininglinestotheGradienttableEditor.SavethetableasXieHe_dti_026.

4）SettheImageorientationto‘Axial（1,0,0）,（0,1,0）’asmentionedabove.

5）Settheoutputprefix.

6）Markthecheckboxof‘Tracking’.

7）‘Reconprefix’,’Savetrackas’,’Maskimage’arerelated.Thelasttwovalueswillchangeas‘Reconprefix’changes.

8）ChoosetheOrientationpatchas‘x’,’y’,’z’respectivelyandclick‘Run’toseetheresult.TrackViswilllaunchautomaticallyaftertheResconstraction..

9）IgotthebestresultwhenIsettheOrientationpatchtoYforthisstudy.So‘y’istherightoptionin8）.It’saTrailandErrorthing.

3.Createbinarymask

1）Changedirectoryto/usr/test.

2）Copyalltheeddycurrentcorrectedimagefileto/usr/test/eddy:

sudocp./data/E_*.nii.gz./eddy/

3）Changedirectoryto/usr/test/eddy:

cd./eddy

4）Creatafilenamedbet.sh:

sudogeditbet.sh.（editwithEmEditorandExcelinthelocalcomputer,andthencopythecodestotheremotecomputer）.

Hereweneedtochangetheparameterof‘f’（fractionalintensitythreshold（0->1）;default=0.5;smallervaluesgivelargerbrainoutlineestimates）tocheckoutthebest‘f’forthisstudy.Thatistosay,runbet.shadequatetimeswithdifferent‘f’.Ichosen0.25,0.28,0.3and0.5.

5）Runbet.sh4timeswithdifferent‘f’value,checktheresultwithfslview.

Yellow:

f=0.25,Cyan:

f=0.28,Red:

f=0.3,Blue:

f=0.5

Igotthebestresultatf=0.25forthisstudy.

4.Fitthediffusiontensormodelusingdtifit.

1）Changedirectoryto/usr/test.

2）Copyalltheneededfileto/usr/test/bet:

sudocp./data/E_*.nii.gz./bet/

sudocp./eddy/b_f0_25E_*.nii.gz./bet

3）Changedirectoryto/usr/test/datatocheckoutabnormalities

<1>checktheecclogfile

ThesubjectZHANGBINisdifferenttotheothers.

<2>Changedirectoryto/usr/test/XieHe-DTI-Dicomandcheckthe.bvecand.bvalfiles

cd/usr/test/XieHe-DTI-Dicom

more./*/*.bvec

more./*/*.bval

TheyareallthesameforallthesubjectsexceptZHANGBIN.SodiscardthefileofZHANGBINin/use/test/bet.

4）Changedirectoryto/usr/test/bet

cd./bet

5）Copythe.bvecand.bvalfilesto/usr/test/betandrenamethem.

move/usr/test/XieHe-DTI-Dicom/chaiejun/*.bvec./XIEHE.bvec

move/usr/test/XieHe-DTI-Dicom/chaiejun/*.bval./XIEHE.bval

6）Creatafilenameddtifit.sh:

sudogeditditfit.sh.（editwithEmEditorandExcelinthelocalcomputer,andthencopythecodestotheremotecomputer）.Rundtifit.sh

./dtifit.sh

PartIII.RunTBSS

1.CreattwofoldersfordadaprocessingandmovethecorrespondingFAdatatothem.

cd/usr/test

sudomkdirCRCL

cp./bet/control*_FA.nii.gz./CR./CL

cp./bet/p_left_*_FA.nii.gz./CL

cp./bet/p_Right*_FA.nii.gz./CR

2.CreatafilenameTBSS.shandsaveitin./CRand./CL.ThecodesofTBSS.shis

#!

/bin/sh

tbss_1_preproc*.nii.gz

tbss_2_reg-T

tbss_3_postreg-S

exit0

3.RunTBSS.shin./CRand./CL.Thistakes~12hours.

4.checkwhetherasuitablethresholdforthemeanFAskeletonis0.2.

cdstatsfslviewall_FA-b0,0.8mean_FA_skeleton-b0.2,0.8-lGreen

5.Runtbss_4_prestats

tbss_4_prestats0.2

6.voxelwisestatisticsontheskeletonisedFAdata.

cd../statsdesign_ttest2design1425//forCRdesign_ttest2design1438//forCLrandomise-iall_FA_skeletonised-otbss-mmean_FA_skeleton_mask-ddesign.mat-tdesign.con-n500--T2-Vfslview$FSLDIR/data/standard/MNI152_T1_1mmmean_FA_skeleton-lGreen-b0.2,0.8tbss_tstat1-lRed-Yellow-b3,6tbss_tstat2-lBlue-

第二版本：

[DTI/DWI]分享一个DTI/TBSS数据处理流程

DTIAnalysis

1.CopyoverdicomsfromDTIseriestoadtifolderwithineachsubjectsdirectory

a.

cpdicom/312000-XX-*dti/

i.

XX=DTISeries#

2.

mri_convert312000-XX-1.dcmdiffusionseries.nii.gz

a.

output=diffusionseries.mghdti.bvals,diffusionseries.mghdti.bvecs

b.

renamefilesasbvalsandbvecs,respectively

3.

eddy_correctdiffusionseries.nii.gzdata.nii.gz0

4.

mkdirtemp

5.

cpdata.nii.gztemp/

6.

cdtemp

7.

fslsplitdata.nii.gz–t

8.

cpvol0000.nii.gztodtidir

a.

cpvol0000.nii.gz../nodif.nii.gz

9.

betnodif.nii.gznodif_brain–m–v–o–g0.2–f0.3

10.

dtifit–kdata.nii.gz–odti–mnodif_brain_mask–rbvecs–bbvals–V

-Outputincludeseigenvectors,eigenvalues,meandiffusivityandFAmaps

-Ifyouwanttoruntractography,gotothenextstep.

-IfyouwanttorunTractBasedSpatialStatistics（TBSSforFAanalysis）,gotoendofthissection.

11.

runbedpostx（bedpostx./）

a.

Longeststep,takesabout24-48hourstorun.

12.

copyoverMPRAGEseriestodtifolder（candoanytimebeforeregistrationorTBSS!

[12-14]）

a.

cpTrioTim-…/312000-4-*dti/

13.

mri_convert968000-4-1.dcmhighres_brain.nii.gz

14.

bethighres_brain.nii.gzhighres_brain_only

15.

RegistrationSteps

a.

DiffusiontoStructural:

flirt–innodif_brain–refhighres_brain_only.nii.gz–omatdif2highres.mat–searchrx-9090–searchry-9090–searchrz-9090–dof6–costmutualinfo

b.

Structuraltodiffusion:

convert_xfm–omathighres2dif.mat–inversedif2highres.mat

c.

StructuraltoStandard:

flirt–inhighres_brain_only.nii.gz–ref/usr/share/fsl/data/standard/avg152T1_brain.nii.gz–omathighres2standard.mat–searchrx-9090–searchry-9090–searchrz-9090–dof12–costcorratio

d.

StandardtoStructural:

convert_xfm–omatstandard2highres.mat–inversehighres2standard.mat

e.

DiffusiontoStandard:

convert_xfm–omatdif2standard.mat–concathighres2standard.matdif2highres.mat

f.

StandardtoDiffusion:

convert_xfm–omatstandard2dif.mat–inversedif2standard.mat

TBSSWalkthrough

1.

AfterFAmaphasbeencreatedfromdtifit,youarereadytorunTBSSforanalysisonthisdatarunonlywhenALLdatahasbeencollected

2.

Allstepswilltakeplacein/users/fpolli/DTI_STUDY_DIR/dti_tbss

3.

Ifstartingnewanalysis,shouldremoveallpreviousdatafrom

4.

MoveFAimagesfromeachsubjecttothedti_tbssdirectory（makesurepreviousdatahasbeenremoved?

?

）

5.

tbss_1_preproc*.nii.gz

a.

ErodesFAimagesslightlyandremovelikelyoutliersfromdiffusiontensorfitting

b.

Movesallimagesintonewsub-dir（FA）andcreatesdirorigdata

6.

tbss_2_reg–n

a.

–nflagalignseveryFAimagetoeveryotherone,findsthemost“typical”subjectasatargetimageforallotherimagestoalignto

b.

Longstep.Takesabout20minutes/registration

7.

tbss_3_postreg–S

a.

appliesnonlineartransformsfromthestepabovetobringthemintostandardspace

b.

–S:

derivesthemeanFAandskeletonfromyoursubjects

c.

–T:

usestheFMRIB58_FAmeanFAimageanditsskeletonratherthanyoursubjects

8.

fslviewall_FA.nii.gz–b0,0.8mean_FA_skeleton.nii.gz–b0.2,0.8–lGreen

9.

tbss_4_prestats0.2

a.

.2isthresholdtomakesuregreymatter,ventriclesaren’tincluded

b.

Togetstatistics,mustcreatedesignmatrixandcontrastmatrix

10.

design_ttest2designXY

a.

X–