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+
> >
>
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