[Mristudio-users] using T1 image for ROI drawing

Fri Jul 16 21:45:19 EDT 2010

Hi Aifeng,

As I mentioned in another thread, AIR/MUT in DtiStudio is designed for
intra-DTI motion correction. Suppose you have 1 b0 and 30 DWIs, all DWIs can
be registered to the b0.

In your case, you want to do cross-modality (T1 vs DTI) registration. I
recommend you to use DiffeoMap for that purpose. This program is designed
for intra-subject cross-modality (the same person, different scans) or
inter-subject image registration, which you are interested in.

The "adjust the gradient ..." option is for intra-DTI registration. If each
DWI is not registered and motion-corrected, you need to recalculate the
gradient table, strictly speaking. We usually do not use this option, but
sometime reviewers ask if you recalculate the table.

On Fri, Jul 9, 2010 at 4:49 PM, Zhang, Aifeng <azhang at psych.uic.edu> wrote:

>  Dear DTIStudio,
>
>
>
> Just want to double check with you about my procedure with one DTI sequence
> and one MPRAGE:
>
>
>
> In DTIStudio:
>
> 1) MRI view3D: register MPRAGE image (voxel size 0.83X0.83X1.1mm) to b0
> image (0.83X0.83X2.2mm) using affine transformation.
>
> 2) DTI Mapping: register all DWIs to b0 using affine too.
>
> 3) Fiber-tracking: draw ROI on co-registered MPRAGE images for fiber
> tracking.
>
>
>
> in step 2:  do you recommend choosing the option of "Adjusting the
> gradients of the DWI images if applicable"???
>
>
>
> thanks for your help!
>
>
>
> Sincerely,
>
> Aifeng
>
>
>
> *From:* smoriw at gmail.com [mailto:smoriw at gmail.com] *On Behalf Of *susumu
> mori
> *Sent:* Thursday, July 08, 2010 8:01 PM
> *To:* Zhang, Aifeng
> *Subject:* Re: [Mristudio-users] Eddy_current_correction
>
>
>
> Yes. Usually all DWIs to b0.
>
> On Thu, Jul 8, 2010 at 8:37 PM, Zhang, Aifeng <azhang at psych.uic.edu>
> wrote:
>
> Dr. Mori,
>
>
>
> thanks for quick response.  So I will register 32 gradients to b0 for all
> my data.
>
>
>
> I don't have error message problem.  (maybe it's someone else?)
>
>
>
> thanks!
>
> Aifeng
>
>
>
> *From:* smoriw at gmail.com [mailto:smoriw at gmail.com] *On Behalf Of *susumu
> mori
> *Sent:* Thursday, July 08, 2010 7:30 PM
> *To:* Zhang, Aifeng
>
>
> *Subject:* Re: [Mristudio-users] Eddy_current_correction
>
>
>
> Do you still have the error message problem?
> Because coregistration smooths the data and SNR changes, it is a good idea
> to apply it to all data.
>
> On Thu, Jul 8, 2010 at 8:08 PM, Zhang, Aifeng <azhang at psych.uic.edu>
> wrote:
>
> Dear DTIStudio,
>
>
>
> Is coregistration always recommended as the first step, as I saw from
> articles from your lab? In our case, we only acquired 1 DTI sequence with 32
> directions (~4 mins, with SENSE 2.5).  thanks.
>
>
>
> Sincerely,
>
> Aifeng
>
>
>
> *From:* mristudio-users-bounces at mristudio.org [mailto:
> mristudio-users-bounces at mristudio.org] *On Behalf Of *susumu mori
> *Sent:* Wednesday, June 30, 2010 9:32 PM
>
>
> *To:* DTI Studio, ROI Editor, DiffeoMap Questions/Support
> *Subject:* Re: [Mristudio-users] Eddy_current_correction
>
>
>
> When you load the REC file using "Mri3DView", make sure how many images are
> in the file. For example, if you used Philips "High" table, you have 1 b0 +
> 32 DWI + 1 extra image, total 34 images. The last one is an
> isotropically-weighted image generated from the DWIs. Then make sure your
> gradient table. Most likely, the number of images in your REC and the
> gradient table are not matching.
>
> For example, you may have only 33 lines in the table. For the final image,
> which you don't use, you can add an extra line with 33: 100, 100, 100. The
> first "33" is the line number (34th table row), and "100, 100, 100" sends a
> message to DtiStudio "don't use this image".
>
> On Tue, Jun 29, 2010 at 6:19 AM, Seyede Ghazal Mohades <
> Seyede.Ghazal.Mohades at vub.ac.be> wrote:
>
> >Dear all
> I have a completely basic question
> when I try to load Philips Rec images in DTI studio I can do it, however
> the same set file  (which is a DTI ss-EPI sequence )gives the following
> error when I try to do DTI mapping :
> the file is Bigger (and sometimes it says smaller)than a DWI sequence!
> where is the problem?
> regards
> Ghazal
> >Thanks
> >
> >-----Original Message-----
> >From: mristudio-users-bounces at mristudio.org on behalf of
> support at mristudio.org
> >Sent: Mon 6/28/2010 12:24 PM
> >To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
> >Subject: Re: [Mristudio-users] Eddy_current_correction
> >
> >the 1st method would be fine: use the 1st B0 as a reference and register
> all
> >others with it.
> >
> >support
> >
> >
> >
> >>
> >> Hi All,
> >>
> >> We have diffusion data set acquired with 5 trails/repetitions(in single
> time
> >> point/cross sectional) for each and every subject. This means i have 5
> b0(same
> >> value) and DW (12 directions) data while doing eddy current correction
> can i
> >> choose for instance b0 from first trail and register all the DW and
> other b0
> >> images to this or do eddy current correction separately for each and
> every trail
> >> and finally register all of them together say for instance to the first
> trail.
> >>
> >> Thanks
> >>
> >> venkat
> >>
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> >Cleveland Clinic is ranked one of the top hospitals
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