def tracks_in_cm_roi(): froi='/home/eg309/Data/ICBM_Wmpm/ICBM_WMPM.nii' wI=get_roi(froi,35,1) #4 is genu #c=get_cm_roi2(froi,[35]) fname='/home/eg309/Data/PROC_MR10032/subj_03/101/1312211075232351192010092217244332311282470ep2dadvdiffDSI10125x25x25STs004a001_QA_warp.dpy' dpr=Dpy(fname,'r') T=dpr.read_indexed(range(2*10**4)) print len(T) Troi=[] for t in T: #if track_roi_intersection_check(t,wI,.5): if point_track_sq_distance_check(t,c,4.): Troi.append(t) print(len(Troi)) dpr.close() from dipy.viz import fos r=fos.ren() fos.add(r,fos.line(Troi,fos.red)) fos.add(r,fos.point(wI,fos.green)) fos.add(r,fos.sphere(c,2.)) fos.show(r)
def warp_tracks(): dn='/home/eg309/Data/TEST_MR10032/subj_03/101/' ffa=dn+'1312211075232351192010092217244332311282470ep2dadvdiffDSI10125x25x25STs004a001_bet_FA.nii.gz' finvw=dn+'1312211075232351192010092217244332311282470ep2dadvdiffDSI10125x25x25STs004a001_warps_in_bet_FA.nii.gz' fqadpy=dn+'1312211075232351192010092217244332311282470ep2dadvdiffDSI10125x25x25STs004a001_QA_native.dpy' flaff=dn+'1312211075232351192010092217244332311282470ep2dadvdiffDSI10125x25x25STs004a001_affine_transf.mat' fref ='/usr/share/fsl/data/standard/FMRIB58_FA_1mm.nii.gz' fdis =dn+'1312211075232351192010092217244332311282470ep2dadvdiffDSI10125x25x25STs004a001_nonlin_displacements.nii.gz' fdis2 =dn+'1312211075232351192010092217244332311282470ep2dadvdiffDSI10125x25x25STs004a001_nonlin_displacements_withaff.nii.gz' #read some tracks dpr=Dpy(fqadpy,'r') T=dpr.read_indexed(range(150)) dpr.close() #from fa index to ref index res=flirt2aff_files(flaff,ffa,fref) #load the reference img imgref=ni.load(fref) refaff=imgref.get_affine() #load the invwarp displacements imginvw=ni.load(finvw) invwdata=imginvw.get_data() invwaff = imginvw.get_affine() #load the forward displacements imgdis=ni.load(fdis) disdata=imgdis.get_data() #load the forward displacements + affine imgdis2=ni.load(fdis2) disdata2=imgdis2.get_data() #from their difference create the affine disaff=imgdis2.get_data()-disdata shift=np.array([disaff[...,0].mean(),disaff[...,1].mean(),disaff[...,2].mean()]) shape=ni.load(ffa).get_data().shape disaff0=affine_transform(disaff[...,0],res[:3,:3],res[:3,3],shape,order=1) disaff1=affine_transform(disaff[...,1],res[:3,:3],res[:3,3],shape,order=1) disaff2=affine_transform(disaff[...,2],res[:3,:3],res[:3,3],shape,order=1) disdata0=affine_transform(disdata[...,0],res[:3,:3],res[:3,3],shape,order=1) disdata1=affine_transform(disdata[...,1],res[:3,:3],res[:3,3],shape,order=1) disdata2=affine_transform(disdata[...,2],res[:3,:3],res[:3,3],shape,order=1) #print disgrad0.shape,disgrad1.shape,disgrad2.shape #disdiff=np.empty(invwdata.shape) #disdiff[...,0]=disgrad0 #disdiff[...,1]=disgrad1 #disdiff[...,2]=disgrad2 #ni.save(ni.Nifti1Image(disdiff,invwaff),'/tmp/disdiff.nii.gz') di=disdata0 dj=disdata1 dk=disdata2 d2i=invwdata[:,:,:,0] + disaff0 d2j=invwdata[:,:,:,1] + disaff1 d2k=invwdata[:,:,:,2] + disaff2 #di=disgrad0 #dj=disgrad1 #dk=disgrad2 imgfa=ni.load(ffa) fadata=imgfa.get_data() faaff =imgfa.get_affine() Tw=[] Tw2=[] Tw3=[] froi='/home/eg309/Data/ICBM_Wmpm/ICBM_WMPM.nii' roiI=get_roi(froi,3,1) #3 is GCC roiI2=get_roi(froi,4,1) #4 is BCC roiI3=get_roi(froi,5,1) #4 is SCC roiI=np.vstack((roiI,roiI2,roiI3)) for t in T: if np.min(t[:,2])>=0:#to be removed mci=mc(di,t.T,order=1) #interpolations for i displacement mcj=mc(dj,t.T,order=1) #interpolations for j displacement mck=mc(dk,t.T,order=1) #interpolations for k displacement D=np.vstack((mci,mcj,mck)).T WI=np.dot(t,res[:3,:3].T)+res[:3,3]+D#+ shift W=np.dot(WI,refaff[:3,:3].T)+refaff[:3,3] mc2i=mc(d2i,t.T,order=1) #interpolations for i displacement mc2j=mc(d2j,t.T,order=1) #interpolations for j displacement mc2k=mc(d2k,t.T,order=1) #interpolations for k displacement D2=np.vstack((mc2i,mc2j,mc2k)).T WI2=np.dot(t,res[:3,:3].T)+res[:3,3]+D2 #+ shift W2=np.dot(WI2,refaff[:3,:3].T)+refaff[:3,3] WI3=np.dot(t,res[:3,:3].T)+res[:3,3] W3=np.dot(WI3,refaff[:3,:3].T)+refaff[:3,3] Tw.append(W) Tw2.append(W2) Tw3.append(W3) from dipy.viz import fos r=fos.ren() fos.add(r,fos.line(Tw,fos.red)) fos.add(r,fos.line(Tw2,fos.green)) fos.add(r,fos.line(Tw3,fos.yellow)) fos.add(r,fos.sphere((0,0,0),10,color=fos.blue)) fos.add(r,fos.point(roiI,fos.blue)) fos.show(r)