[Mristudio-users] b-matrix from dicom header and from techs
Xin Li
xli16 at jhmi.edu
Mon Jul 19 17:13:47 EDT 2010
Hello Venkateswaran,
For your fourth question, it may be because that your computer doesn't have the Microscoft Visual Studio redistribution package. Please download vcredist_x86.exe at https://www.mristudio.org/wiki/installation and install it before you run DtiStudio.
Hope this will solve the problem.
Xin
----- Original Message -----
From: "Rajagopalan, Venkateswaran" <rajagov2 at ccf.org>
Date: Monday, July 19, 2010 5:03 pm
Subject: Re: [Mristudio-users] b-matrix from dicom header and from techs
To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org>
> Dear Dr.Mori,
>
> Sorry to digress little bit but something releveant on the same topic.
>
> 1) What is the DICOM header tag for gradient table information, I
> have Siemens versions from 2004 (VA 25A)and came to know that after
> 2006 they have CSA header info from where you can extract information
> regarding Diffusion data. So for versions of 2004 and older where can
> i find gradient table information.
>
> 2) When i use dcm2nii to extract gradient table information for these
> older software versions it is mentioned by Chris Rorden that he
> appropriately rotates these gradient tables to conform to NIFTI format
> (since dicom and NIFTI coordinates are different). I am using FSL for
> eddy/motion correction and also to rotate bvec after eddy/motion
> correction. I however convert NIFTI to Analyze format and then to dti
> "raw" format and do tensor calculation so i am wondering whether this
> "raw"format has same coordinates as NIFTI.
>
> 3) Do you have an option in DTIstudio to open NIFTI files.
>
> 4) Last one When i try to run DTIstudio-latest-x86.exe it gives me
> the following error "This application failed to start because the
> application configuration is incorrect. Reinstalling the application
> may fix this problem". Any help on this would be greatly appreciated.
>
> Thanks
>
> Venkateswaran
>
> ________________________________
>
> From: mristudio-users-bounces at mristudio.org on behalf of susumu mori
> Sent: Fri 7/16/2010 10:43 PM
> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
> Subject: Re: [Mristudio-users] b-matrix from dicom header and from techs
>
>
>
>
>
> 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 (> )
> 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<>> 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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