[Mristudio-users] b-matrix from dicom header and from techs
susumu mori
susumu at mri.jhu.edu
Fri Jul 16 22:43:44 EDT 2010
>
> *1) From the DICOM header of the b0 images, the corresponding gradient
> direction is not (0,0,0). However, it is (0, 0.7,0.7). What does this mean?
> Which one is the right one to use?* *
> *
> Could you send me (susumu at mri.jhu.edu) the copy of the extracted table? We
can take a look.
> * *
> *2) You said that we have to use the gradient table from the DICOM header
> instead of the Manufacturer's table since the former is more accurate.
> So,does this mean that we do not need to load the predefined tables any
> more? Is this true for different scanner software versions or for only VB17?
> *
>
> You can use the generic table but it is much easier to extract the
gradient information from DICOM headers because the gradient signs are
correct and you don't have to do the "flip X" operation after tensor
calculation. Also, it is supposed to be a bit more accurate.
> If you use the table extraction function, you no longer need the
predefined table.
> *3) There is one point that is puzzling me. You said previously that we do
> not need to reorient the gradient table if we are using software version
> after VB15. However, I do not understand what do you mean exactly by this
> sentence?*
>
> "*The are some mixed information about whether we need to reorient
> gradient tables when oblique imaging is used (whether we need to check
> "rotate if applicable" option or not). We are testing it but with the
> scanner we tested last time (VB17 operating system), we needed to check to
> this option.* "
>
> > There is possibility that we misinformed you regarding the necessity of
table rotation for VB15.
> We are also very puzzled that we recently encountered data that requires
gradient rotation. There are two issues;
>> Issue 1: is the gradient table rotated with oblique angle?
>> Issue 2: what is the coordinate system of the table information in the
DICOM header? Is it in the physical X/Y/Z gradient coordinates or image
coordinates? These two coordinates are not the same if the imaging plane is
rotated.
> For your self-defense, I would suggest you to do the following tests. It
is difficult for us to test all manufacturers, all versions, and all image
protocols. So we would appreciate your help;
>> you can scan a person using a plane axial (the brain should look
upright). Then rotate FOV by 30-40 degree and scan again. The brain should
look tilted in the image. Ask the person to rotate the brain by 30-40 degree
and rotate the FOV so that the brain look upright in the image. Scan again.
>> Please process these 3 DTI data.
>> I would appreciate it if you could send the data to us too.
> *Does this mean that we may need to rotate the gradient table in case of
> oblique acquisition for VB17?
>
> *Thank you very much.
>
> Fatma.
>
>
> On Mon, Jul 12, 2010 at 7:59 PM, susumu mori <susumu at mri.jhu.edu> wrote:
>
>> Hi all,
>>
>> For Siemens users, now a new function to extract a gradient table from
>> Mosaic file header is available. The extracted gradient table is usually
>> different from the generic gradient table provided by Siemens from the
>> following points;
>>
>> > X/Y/Z gradient signs (+/-) are dynamically changed based on image
>> protocol (e.g. axial/sagittal/coronal). The extracted tables have correct
>> signs.
>> > The extracted table is more exact because it includes not only the
>> diffusion-weighing gradients but also a small contribution of imaging
>> gradients.
>>
>> The are some mixed information about whether we need to reorient gradient
>> tables when oblique imaging is used (whether we need to check "rotate if
>> applicable" option or not). We are testing it but with the scanner we tested
>> last time (VB17 operating system), we needed to check to this option.
>>
>> We will follow up this issue soon but we strongly recommend you to test
>> your scanner. It can be easily tested by scanning a person twice. Once with
>> a regular axial and one with a strong oblique (30-45 degree). If you are not
>> sure about your results, you can send us your results for check.
>>
>> Susumu
>>
>>
>> On Mon, Jul 12, 2010 at 9:56 AM, Hangyi Jiang <hjiang at jhmi.edu> wrote:
>>
>>> hi, Jeff,
>>>
>>> if the files are in Mosaic format, DtiDtudio can get the gradients from
>>> the header.
>>> below, I attached the email I sent to Venkat for your reference.
>>>
>>> regards,
>>>
>>> hangyi
>>>
>>>
>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>> Hi Venkat,
>>>
>>> this is one of the most confusions to deal with DICOM files.
>>>
>>> according the DICOM standard and Siemens documentation, the gradients
>>> (bvec as you mentioned) in DICOM header should be defined in patient space
>>> (or image matrix space), so the one from dcm2nii should be correct for your
>>> dataset.
>>>
>>> the 1st one (from your MR techs) seems that it is the original definition
>>> based on scanner's coordinate system. this one should be adjusted
>>> dynamically during scanning according to patient position and orientation.
>>> by the way, we usually named it as gradient table, not b-matrix. b-matrix
>>> has 6 components for each of DWIs. b-matrix can be calculated from the
>>> gradient table.
>>>
>>> as a matter of fact, Siemens also saves adjusted b-matrix in the DICOM
>>> header. if you like, you can also use the adjusted b-matrix from the header
>>> for tensor calculation. in fact, using adjusted b-matrix is recommended by
>>> Siemens since it also considered other factors (like gradient cross-over
>>> effects) for image acquisition.
>>>
>>> hope it helps.
>>>
>>> hangyi
>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>
>>>
>>>
>>> ________________________________________
>>> From: mristudio-users-bounces at mristudio.org [
>>> mristudio-users-bounces at mristudio.org] On Behalf Of Jeff Sadino [
>>> jsadino.queens at gmail.com]
>>> Sent: Saturday, July 10, 2010 10:51 PM
>>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support;
>>> rajagov2 at ccf.org
>>> Subject: Re: [Mristudio-users] b-matrix from dicom header and from techs
>>>
>>> Hi Venkat,
>>>
>>> We had the same question on our Siemens VA25A DTIs. The Siemen's tech
>>> support recommended a program called MRIConvert (
>>> http://lcni.uoregon.edu/~jolinda/MRIConvert/<http://lcni.uoregon.edu/%7Ejolinda/MRIConvert/>)
>>> to extract the gradients. I don't have our tables in front of me, but the
>>> .8, 0, and .4 values seem pretty close to what I remember. Siemens said
>>> that they suspected the 1, 0, .5 values were in the scanner direction and
>>> the .8, 0, .4 values were in the patient direction, since I think Siemens
>>> automatically adjusts for that. Just be careful when using the MRIConvert
>>> program to extract gradients, since it flips the y sign for FSL purposes.
>>>
>>> Cheers,
>>> Jeff
>>>
>>> On Fri, Jul 9, 2010 at 9:33 AM, Rajagopalan, Venkateswaran <
>>> rajagov2 at ccf.org<mailto:rajagov2 at ccf.org>> wrote:
>>>
>>>
>>> Dear All,
>>>
>>> we collect our data from Siemens scanner. I got b-matrix from our MR
>>> techs for software version VA25A b matrix is as follows
>>>
>>> 0: 0.000, 0.000, 0.000
>>> 1: 1.000, 0.000, 0.500
>>> 2: 0.000, 0.500, 1.000
>>> 3: 0.500, 1.000, 0.000
>>> 4: 1.000, 0.500, 0.000
>>> 5: 0.000, 1.000, 0.500
>>> 6: 0.500, 0.000, 1.000
>>> 7: 1.000, 0.000, -0.500
>>> 8: 0.000, -0.500, 1.000
>>> 9: -0.500, 1.000, 0.000
>>> 10: 1.000, -0.500, 0.000
>>> 11: 0.000, 1.000, -0.500
>>> 12: -0.500, 0.000, 1.000
>>>
>>> I used dcm2nii software (to convert hem into nifti file for soem other
>>> purpose i also gives me bvec and bval files) which gives me the following
>>> matrix from the dicom header file
>>>
>>> 0 0 0
>>> 0.89 0 -0.45
>>> 0 0.45 -0.89
>>> 0.45 0.89 0
>>> 0.89 0.45 0
>>> 0 0.89 -0.45
>>> 0.45 0 -0.89
>>> 0.89 0 0.45
>>> 0 -0.45 -0.89
>>> -0.45 0.89 0
>>> 0.89 -0.45 0
>>> 0 0.89 0.45
>>> -0.45 0 -0.89
>>>
>>> Since not only the values are different but +/- signs are also different
>>> in DW directions. So I am wondering whether any one could tell me which is
>>> the correct table to go with.
>>>
>>> Thanks
>>>
>>> Venkat
>>>
>>>
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