[Mristudio-users] b-matrix from dicom header and from techs
Rajagopalan, Venkateswaran
rajagov2 at ccf.org
Mon Jul 19 17:03:30 EDT 2010
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 (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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