[Mristudio-users] NifTi and DTI Studio

Mon Aug 31 12:20:29 EDT 2009

Hi venkateswaran

1) It seems the DtiStudio version currently posted in
www.mristudio.orgalready 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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