 |
 |
Thank you Matt. ----- Original Message ----- From: Matt Glasser <[log in to unmask]> Date: Wednesday, October 29, 2008 1:32 pm Subject: Re: [FSL] Bad header info of DTI sequence after registered to mprage To: [log in to unmask] > You really shouldn't move the DTI data out of native space and then do > calculations like DTIFIT or BEDPOSTX on it. Better to create the > transformation matrices between your diffusion space and structural > spaceusing the FA image (from DTIFIT) and your mprage using the > FLIRT -omat > option. The FA image has more similar contrast to the mprage than > the b0, > so it sometimes provides a better registration. You can also > invert a > matrix using convert_xfm -inverse option. Then if you want to > specify your > seeds in mprage space and have your results displayed there for > tractography, you need only to specify the transformation matrix > betweenstructural and diffusion space in your probtrackx > commandline using the > --xfm option. > > Similarly, you could generate your tissue partial volume map (or > tissueprobability map) using FAST in structural space, and then > downsample & > transform that map to diffusion space and threshold it at >35% gray > matteras your mask of the cortical regions. Or you could keep > things in > structural space, draw your ROIs there, and use the method above to > incorporate the transform into probtrackx. > > If, for some reason, you do have to move your DTI data into another > spacebefore calculating DTIFIT or BEDPOSTx, you will have to rotate > the gradient > table according to any rotations applied when moving from native > DTI space > to other space. > > Peace, > > Matt. > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On > BehalfOf Xin Li > Sent: Wednesday, October 29, 2008 1:03 PM > To: [log in to unmask] > Subject: Re: [FSL] Bad header info of DTI sequence after registered to > mprage > > Hi Mark, > > Thank you for your explaination. We have averaged across multiple > acqusitions and done eddy_correct for the diffusion series. I guess > we don't > have to do registration at this stage. We can go ahead to run > dtifit and > bedpostx as suggested in the pipeline. But then it'll come back to > registration (step 5 in FSL pipleline) after bedpostx. If I > understandcorrectly, "do a separate registration to the structural > volume" still > requires downsampling the mprage structural volume, right? > > Actually, we are trying to follow the method mentioned in Croxson > et al's > paper. We came to this point, > > "We thresholded the results to include only voxels > estimated at >35% gray matter and used this to mask the cortical > regions.We skull stripped the diffusion-weighted and T1-weighted > images(Smith, 2002) and performed affine coregistration (Jenkinson and > Smith, 2001)" ( Croxson et al J. Neurosci., September 28, 2005 . > 25(39):8854-8866 (full text attached below) ) > > That is why I am trying to register the diffusion series to the mprage > volume. Does it make sense to do registration before bedpostx? > > Again, thank you for your input. > Rick > > Method: > "We corrected the human diffusion data for eddy currents and head > motion using affine registration to a reference volume (Jenkinson and > Smith, 2001). The data from the three acquisitions were subsequently > averaged to improve the signal-to-noise ratio. > We performed tissue-type segmentation, skull stripping, and > registrationon the scans, using tools from the Oxford Centre for > FunctionalMagnetic Resonance Imaging of the Brain's (FMRIB) > Software Library > (www.fmrib.ox.ac.uk/fsl). We performed probabilistic tissue-type > segmentation > and partial volume estimation on the T1-weighted image > (Zhang et al., 2001). We thresholded the results to include only > voxelsestimated at >35% gray matter and used this to mask the > cortical regions. > We skull stripped the diffusion-weighted and T1-weighted images > (Smith, 2002) and performed affine coregistration (Jenkinson and > Smith, 2001) between the first nondiffusion-weighted volume and the > T1-weighted image to derive the transformation matrix between the two > spaces. We then calculated probability distributions of fiber > direction at > each voxel using previously described methods (Behrens et al., > 2003a)."(Croxson et al.) > > > ----- Original Message ----- > From: Mark Jenkinson <[log in to unmask]> > Date: Wednesday, October 29, 2008 1:18 pm > Subject: Re: [FSL] Bad header info of DTI sequence after registered to > mprage > To: [log in to unmask] > > > Hi Rick, > > > > The reference image controls the final output dimensions and > voxel > > size.The -noresample flag just controls whether the input image > is > > internallyresampled to regular 8mm, 4mm, 2mm and 1mm grids, or > > forced to stay > > at its native resolution. However, the final creation of the > > output > > image > > will still use whatever is specified by the reference volume. > > > > Now one question is do you need your diffusion images aligned > with > > yourmprage at this point? We normally just correct for motion > > effects > > within > > the diffusion series using eddy_correct (which aligns them to one > > of the > > unweighted images in your series) and then do a separate > registration> to the structural volume later, with the option of > displaying your > > > > diffusion > > analyses in either native diffusion space or structural space. > > Have a > > look > > at the FDT documentation to see what the standard arrangements are. > > > > If you are not happy with the standard pipeline and do need to align > > your diffusion images directly to your mprage, then you need to > > initially > > make a downsampled version of your mprage, and then use this as the > > reference volume in all the -applyxfm calls for flirt. You can > do the > > downsampling with the ApplyXFM tool. > > > > I hope this answers your questions. > > All the best, > > Mark > > > > > > On 29 Oct 2008, at 17:06, Xin Li wrote: > > > > > Hi Mark, > > > > > > I tried the "-noresample" option to stop FLIRT from upsampling > > the > > > input, yet Flirt still outputs the upsampled 160x512x512x1 vol. > > > > Should I try something else? > > > > > > Command: > > > flirt -noresample -in DTIVol0000.nii.gz -ref mprage.nii.gz - > > applyxfm > > > -init NodiffusionRegToMprageMat -out DTIRegToMprageVol0000 > > > > > > DTIVol0000 is 128x128x66x1, mprage is 160x512x512x1 and > > > DTIRegToMprageVol0000 is 160x512x512x1 instead of 128x128x66x1. > > > > > > Thanks, > > > Rick > > > ----- Original Message ----- > > > From: Mark Jenkinson <[log in to unmask]> > > > Date: Tuesday, October 28, 2008 4:26 pm > > > Subject: Re: [FSL] Bad header info of DTI sequence after > > registered > > > to mprage > > > To: [log in to unmask] > > > > > >> Hi, > > >> > > >> It sounds like the fslmerge command did not run successfully as > > >> it probably ran out of memory. Is there any reason that you want > > >> you 4D diffusion images upsampled to 0.5x0.5x1mm? We normally > > >> recommend doing all diffusion analysis in the native diffusion > > space.>> > > >> The upsampled data, being 512x512x160x65 would take up 5GB > > >> of memory, plus extra if any temporary copies or partial > copies are > > >> needed inside the code, which is probably why it currently fails. > > >> > > >> All the best, > > >> Mark > > >> > > >> > > >> > > >> > > >> On 28 Oct 2008, at 20:17, Xin Li wrote: > > >> > > >>> Dear FSL Users, > > >>> > > >>> I am trying to register the DTI sequence (FLIRT) to a mprage vol > > >> so > > >>> that we can utilize the mask created from the mprage. > > >>> > > >>> Here is what I did: > > >>> > > >>> 1. extract the 3D no-diffusion vol from the DTI sequence(4D). > > >> (Both > > >>> are already skull stripped) > > >>> > > >>> 2. register the no-diffusion vol to the mprage and save the > > >>> transformation matrix: > > >>> > > >>> flirt -in nodiffusion.nii.gz -ref mprage.nii.gz -out > > >>> NodiffusionRegToMprage.nii.gz -omat NodiffusionRegToMprageMat > > >>> > > >>> 3. Align all DTI volumes to the mprage volume using the saved > > >> matrix:> > > >>> flirt -in DTIVol0000.nii.gz -ref mprage.nii.gz -applyxfm -init > > >>> NodiffusionRegToMprageMat -out > > >>> DTIRegToMprageVol0000 > > >>> > > >>> 4. Then create a new 4D DTI sequence from the registered volumes > > >>> fslmerge -a DTIRegToMprage DTIRegToMprageVol* > > >>> > > >>> All steps completed successfully except that the new 4D DTI > > >> sequence > > >>> (DTIRegToMprage) has "bad header info". Could anyone tell me > > >> what > > >>> causes this? > > >>> > > >>> Many Thanks, > > >>> > > >>> Rick > > >>> > > >>> All header info are attached below FYI: > > >>> 1.Old DTI sequence (4D) > > >>> data_type INT16 > > >>> dim1 128 > > >>> dim2 128 > > >>> dim3 66 > > >>> dim4 65 > > >>> datatype 4 > > >>> pixdim1 2.0000000000 > > >>> pixdim2 2.0000000000 > > >>> pixdim3 2.0000000000 > > >>> pixdim4 1.0000000000 > > >>> cal_max 3915.0000 > > >>> cal_min 0.0000 > > >>> file_type NIFTI-1+ > > >>> > > >>> 2. no-diffusion vol(3D) > > >>> data_type INT16 > > >>> dim1 128 > > >>> dim2 128 > > >>> dim3 66 > > >>> dim4 1 > > >>> datatype 4 > > >>> pixdim1 2.0000000000 > > >>> pixdim2 2.0000000000 > > >>> pixdim3 2.0000000000 > > >>> pixdim4 1.0000000000 > > >>> cal_max 3915.0000 > > >>> cal_min 0.0000 > > >>> file_type NIFTI-1+ > > >>> > > >>> 3.Mprage > > >>> data_type FLOAT32 > > >>> dim1 160 > > >>> dim2 512 > > >>> dim3 512 > > >>> dim4 1 > > >>> datatype 16 > > >>> pixdim1 1.0000000000 > > >>> pixdim2 0.5000000000 > > >>> pixdim3 0.5000000000 > > >>> pixdim4 1.0000000000 > > >>> cal_max 0.0000 > > >>> cal_min 0.0000 > > >>> file_type NIFTI-1+ > > >>> > > >>> 4.Register no-diffusion vol > > >>> data_type INT16 > > >>> dim1 160 > > >>> dim2 512 > > >>> dim3 512 > > >>> dim4 1 > > >>> datatype 4 > > >>> pixdim1 1.0000000000 > > >>> pixdim2 0.5000000000 > > >>> pixdim3 0.5000000000 > > >>> pixdim4 1.0000000000 > > >>> cal_max 3915.0000 > > >>> cal_min 0.0000 > > >>> file_type NIFTI-1+ > > >>> > > >>> 5.Registered diffusion vols > > >>> data_type INT16 > > >>> dim1 160 > > >>> dim2 512 > > >>> dim3 512 > > >>> dim4 1 > > >>> datatype 4 > > >>> pixdim1 1.0000000000 > > >>> pixdim2 0.5000000000 > > >>> pixdim3 0.5000000000 > > >>> pixdim4 1.0000000000 > > >>> cal_max 3915.0000 > > >>> cal_min 0.0000 > > >>> file_type NIFTI-1+ > > >>> > > >> > > > > > >