[Mristudio-users] NifTi and DTI Studio

Mon Aug 31 12:52:40 EDT 2009

Dear Dr.Mori,

Thanks for your kind information.

As for the "distortion correction", do you mean Eddy current distortion correction or B0 susceptibility correction? If the former is the case, you can use the Affine tool in DtiStudio.

Sorry i was not clear earlier,  it is B0 suspectibily artifacts correction.

As for the b-matrix rotation, do you mean the rotation for oblique-angle imaging that affect older Siemens system?

Yes, our scanners are seimens scanners.

Read Mosaic/Dicom directly to DtiStudio, provide the Siemens-provide original b-table, click the "rotation if applicable", and load the data.
Close the window and re-open the data input window. There you can find that b-table of the previous session still remembered by DtiStudio. This table is already rotated (not the original b-table anymore). You can use this table for the Raw data.

Thanks for this information i also thought about this, but one question prevented me from doing this, i would like to clarify that with you, after distortion correction especially the voxels in frontal regions of the brain like corpus callosum ( i am not good in anatomy sorry apologize me if i am wrong) are streched or in other words restored to their original positions, so i am wondering whether this kind of voxel stretching and squeezing (undistorted) will contribute to any additional changes in b-matrix when compared to the changes in b-mtarix contributed by the original i.e distorted images. I understand that b-matrix rotation i calculated from the rotation matrix of the main affine matrix, i don't know whether the affine matrix will be different between before and after distortion correction images. I am sorry if i am not clear.  

The b-table rotation option for oblique imaging doesn't work for Raw/Analyze/Nifty in DtiStudio. Do Analyze and Nifty have a field for oblique angles? 

I am sorry Dr.Mori i don't whether Analyze and Nifti has fields for oblique angles.

Thanks again for your help.

Regards
venkateswaran

________________________________

From: mristudio-users-bounces at mristudio.org on behalf of susumu mori
Sent: Mon 8/31/2009 12:20 PM
To: DTI Studio, ROI Editor, Landmarker Questions/Support; Hangyi Jiang
Subject: Re: [Mristudio-users] NifTi and DTI Studio

Hi venkateswaran

1) It seems the DtiStudio version currently posted in www.mristudio.org <http://www.mristudio.org/>  already has the function to read/write Nifty. Please check and send me feedbacks if you encounter and problems.
2) As for the "distortion correction", do you mean Eddy current distortion correction or B0 susceptibility correction? If the former is the case, you can use the Affine tool in DtiStudio.
3) As for the b-matrix rotation, do you mean the rotation for oblique-angle imaging that affect older Siemens system? If that is the case, it would be a complicated issue. The easiest way is, to read the Dicom/Mosaic directly to DtiStudio, which can automatically recalculate the b-table based on the oblique information in the header. Once you go through FLS and data is converted to Nifty/Analyze/Raw, the oblique information is lost. You can still trick DtiStudio in the following way, but it is a bit cumbersome. 

> Read Mosaic/Dicom directly to DtiStudio, provide the Siemens-provide original b-table, click the "rotation if applicable", and load the data.
> Close the window and re-open the data input window. There you can find that b-table of the previous session still remembered by DtiStudio. This table is already rotated (not the original b-table anymore). You can use this table for the Raw data.

4) The b-table rotation option for oblique imaging doesn't work for Raw/Analyze/Nifty in DtiStudio. Do Analyze and Nifty have a field for oblique angles? If so, maybe Hangyi wants to see if we can make the option available for Analyze and Nifty.

On Mon, Aug 31, 2009 at 11:49 AM, Rajagopalan, Venkateswaran <rajagov2 at ccf.org> wrote:

	Dr.Mori,

	Sorry to intrude in Yuzheng's question section. I have the following question, i am using FSL to perform distortion correction of DTI images, after this i convert them into analyze format and open them in DTI studio and save them as RAW format and then run "DTI mapping" to calculate FA and other metrics, in answersing to a question in the forum on b-matrix rotation you have indicated that with "RAW" format we cannot actually perform b-matrix rotation option. Now the only way for me to bring the distortion corrected images from FSL is by analyze format and save as RAW format so in this case i am not able to do this b-matrix rotation, in some of my data i observed that b-matrix is significantly rotated so i prefer to check the b-matrix  rotation option in my data sets. Any suggestion on this.

	Thanks in advance,

	Regards
	venkateswaran

	________________________________

	From: mristudio-users-bounces at mristudio.org on behalf of susumu mori
	Sent: Sat 8/29/2009 6:27 PM
	To: DTI Studio, ROI Editor, Landmarker Questions/Support; Hangyi Jiang; Xin Li
	Subject: Re: [Mristudio-users] NifTi and DTI Studio

	There is a newer version of DtiStudio that can read Nifty.
	Hangyi and Xin, please work on posting the latest version with updated features.
	We'll notify users once a newer version is available on the web.

	On Wed, Aug 26, 2009 at 12:22 PM, ??? <huyuzheng at gmail.com> wrote:

	               I use FSL to change nifti format to analyze and then use DTI Studio to change analyze to dat format.

	       Did you realy make it? I have used the same way but failed...
	       If NIFITI files could be imported directly into the DTIStudio, it will be wonderful. Hope some make it.

	       Yuzheng

	               JY

	________________________________

	               From: [Seongjin] <choisj70 at gmail.com>
	               To: "DTI Studio, ROI Editor, Landmarker Questions/Support" <mristudio-users at mristudio.org>
	               Sent: Wednesday, August 26, 2009 5:37:58 AM
	               Subject: [Mristudio-users] NifTi and DTI Studio

	               Dear all,

	               Is there anybody know how to import NifTi format data into DTI Studio?

	               -SC

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Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.

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only by the individual or entity to which it is addressed
and may contain information that is privileged,
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law.  If the reader of this message is not the intended
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