Re: [Freesurfer] TRACULA niftii file

[Anastasia Yendiki]

Hi Gabor - The input DWIs can be in any format that can be read by 
mri_convert, including the NIfTI format. The gradient directions should be 
in voxel coordinates, like the ones used by FSL. I don't have experience 
with dcm2nii, but if you have original DICOM files, you can pass those as 
the input, too.


Hope this helps,
a.y

On Thu, 10 May 2012, Gabor Perlaki wrote:


Dear all,

Is TRACULA able to handle 4D FSL niftii as input for DTI images? Are
bves/bvalues extracted by dcm2nii and MRICro accurate for TRACULA? I think
TRACULA needs the bvecs in the image coordinate system, which is not the
same as scanner coordinate system in case of oblique acquisition. Do I need
to use dcm2nii with correction for slice angulation to 
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Re: [Freesurfer] TRACULA niftii file

[Gabor Perlaki]

Dear Anastasia,

I've the original DICOM files, but it is acquired with the standard Siemens
DTI ep2_diff, and not with the MGH-DTI sequence. Is DTI images acquired
with the standard DTI accurate and TRACULA able to extract the bvals and
bvecs from the dicom files?

Thanks,
Gabor

2012/5/10 Anastasia Yendiki 

>
> Hi Gabor - The input DWIs can be in any format that can be read by
> mri_convert, including the NIfTI format. The gradient directions should be
> in voxel coordinates, like the ones used by FSL. I don't have experience
> with dcm2nii, but if you have original DICOM files, you can pass those as
> the input, too.
>
> Hope this helps,
> a.y
>
>
> On Thu, 10 May 2012, Gabor Perlaki wrote:
>
>  Dear all,
>>
>> Is TRACULA able to handle 4D FSL niftii as input for DTI images? Are
>> bves/bvalues extracted by dcm2nii and MRICro accurate for TRACULA? I think
>> TRACULA needs the bvecs in the image coordinate system, which is not the
>> same as scanner coordinate system in case of oblique acquisition. Do I
>> need
>> to use dcm2nii with correction for slice angulation to
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/**complianceline.
>  If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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Re: [Freesurfer] TRACULA niftii file

[Anastasia Yendiki]

You can specify them by setting bvecfile and bvalfile in your 
configuration file.


On Thu, 10 May 2012, Gabor Perlaki wrote:


Dear Anastasia,

I've the original DICOM files, but it is acquired with the standard Siemens
DTI ep2_diff, and not with the MGH-DTI sequence. Is DTI images acquired with
the standard DTI accurate and TRACULA able to extract the bvals and bvecs
from the dicom files?

Thanks,
Gabor

2012/5/10 Anastasia Yendiki 

  Hi Gabor - The input DWIs can be in any format that can be read
  by mri_convert, including the NIfTI format. The gradient
  directions should be in voxel coordinates, like the ones used by
  FSL. I don't have experience with dcm2nii, but if you have
  original DICOM files, you can pass those as the input, too.

  Hope this helps,
  a.y

  On Thu, 10 May 2012, Gabor Perlaki wrote:

Dear all,

Is TRACULA able to handle 4D FSL niftii as input for
DTI images? Are
bves/bvalues extracted by dcm2nii and MRICro
accurate for TRACULA? I think
TRACULA needs the bvecs in the image coordinate
system, which is not the
same as scanner coordinate system in case of oblique
acquisition. Do I need
to use dcm2nii with correction for slice angulation
to 



The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
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Re: [Freesurfer] TRACULA niftii file

[Michael Harms]

Hi Gabor,
dcm2nii's default setting for VB17 DICOMs should be to rotate the bvecs
that it returns into the voxel/image axes if you have a modern version of
it.

See item 8 under Sample Datasets of
http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html
for some notes on this issue and a suggested approach for confirming that
your bvecs are correct (albeit in the context of FSL rather than TRACULA,
although the two tools are apparently the same in that each expect the
bvecs to be in voxel/images axes).

cheers,
-MH

>
> Hi Gabor - The input DWIs can be in any format that can be read by
> mri_convert, including the NIfTI format. The gradient directions should be
> in voxel coordinates, like the ones used by FSL. I don't have experience
> with dcm2nii, but if you have original DICOM files, you can pass those as
> the input, too.
>
> Hope this helps,
> a.y
>
> On Thu, 10 May 2012, Gabor Perlaki wrote:
>
>> Dear all,
>>
>> Is TRACULA able to handle 4D FSL niftii as input for DTI images? Are
>> bves/bvalues extracted by dcm2nii and MRICro accurate for TRACULA? I
>> think
>> TRACULA needs the bvecs in the image coordinate system, which is not the
>> same as scanner coordinate system in case of oblique acquisition. Do I
>> need
>> to use dcm2nii with correction for slice angulation to 
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>

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