Hi Rick,
The reference image controls the final output dimensions and voxel size.
The -noresample flag just controls whether the input image is internally
resampled 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 your
mprage 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+
>>>
>>
>
|