[Mristudio-users] Fwd: mristudio-users Digest, Vol 148, Issue 3

Sat Aug 31 15:02:28 EDT 2013

Dear Rotem,

I guess you need to download the atlas. So, each atlas cokes up with its template as well. As a result once you coregister the fa maps with the atlas, you could simply use the point 3 of the previous mail to extract the values of say plic or corpus callosum.

Regards,
Ravi

Sent from my Windows Phone

________________________________
From: Rotem Saar
Sent: 31/08/2013 03:46 PM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] Fwd: mristudio-users Digest, Vol 148, Issue 3

Dear Susumu and Ravi,

Thank you for your help ! I think the best option for me is the third one -
(copying it here)-

3) As Ravi suggested, you can warp our white matter parcellation map to
 your subject image and automatically parcellate the corpus callosum into
 three regions (the genu, body, and splenium of CC).

so my remaining questions (for now) are:

1) From where can I download the atlas ?
2) If can can give a short explanation regarding whether I should or should
not co-register my DTI images to the T1 images ? In what case do we have to
register the diffusion to the anatomy ? i.e., if I want to extract the
Corpus-callosum from each subject and compare the FA value between patients
and controls - Do I have to do this ?

Thanks again for all your help
Rotem

2013/8/29 <mristudio-users-request at mristudio.org>

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> Today's Topics:
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>    1. Re: FA value for regions in the corpus-callusom (Susumu Mori)
>    2. Re: FA value for regions in the corpus-callusom
>       (Kotikalapudi Raviteja)
>    3. Re: FA value for regions in the corpus-callusom (Susumu Mori)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 29 Aug 2013 11:43:38 -0400
> From: Susumu Mori <smoriw at gmail.com>
> Subject: Re: [Mristudio-users] FA value for regions in the
>         corpus-callusom
> To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support"
>         <mristudio-users at mristudio.org>
> Message-ID:
>         <CAEq9apJZ+6Dmu3S2bXB0p9CW0rkiLDzQX3GqVU7K9q_S2K=
> 9UA at mail.gmail.com>
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>
> There are several options depending on what you need;
>
> 1) Do fiber tracking. It seems that you obtained 5 different tracts that
> comprise the corpus callosum. As you mentioned, you can obtain one FA per
> tract. In your case, 5 FA values. Each FA value is the representative FA of
> each tract by avaraging FA values of all voxels inside a tract.
> 2) Instead of calculating a representative FA for each tract by averaging
> all voxels, you can also use the "profile" option, with which, you can
> obtain a FA value at each 2D slice (axial, sagittal, coronal separately).
> 3) As Ravi suggested, you can warp our white matter parcellation map to
> your subject image and automatically parcellate the corpus callosum into
> three regions (the genu, body, and splenium of CC).
>
> Hope one the approaches addresses your need.
>
>
>
>
> On Thu, Aug 29, 2013 at 7:32 AM, Kotikalapudi Raviteja <
> raviteja.kotikalapudi at gmail.com> wrote:
>
> > Dear Rotem,
> >
> > Though I couldn't get you completely, I understand that you need to
> > extract FA values and compare the same between subjects and controls. For
> > this purpose, you could download the JHU parcellation atlas and then use
> > MRICro to extract your ROIs using 'apply intensity to volume' option.
> This
> > particular ROI would then be saved and you could open it for the FA maps
> > and note down the values.
> >
> > I hope this helps, if it is related.
> >
> > Regards,
> > Ravi
> >
> >
> >
> > On Thu, Aug 29, 2013 at 4:29 PM, Rotem Saar <saar.rotem at gmail.com>
> wrote:
> >
> >> Dear experts,
> >>
> >> I have performed Automatic image registration to 19 subjects (who I have
> >> DTI scans for) and now about to begin fiber tracking.
> >>
> >> According to my previous anatomical results, I found volume reductions
> in
> >> specific areas of the corpus callosum, which were correlated to
> behavioral
> >> memory results. I now want to analyze the DTI data, and test for the
> >> correlations between the anatomical volume (per region, 5 in number),
> >> memory performance and FA values (per region, 5 in number).
> >>
> >> In the current working program in DTIstudio I only know how to extract a
> >> singe FA value for the corpuse if this is what I marked for the fiber
> >> tracking. I understand that I can mark a single area in the corpus each
> >> time but that will probably won't be accurate when comparing subjects...
> >>
> >> Is there any way to load a segmentation map in order for DTIstudio to
> >> compute the FA value for each region defined in the map automatically
> >> without the need to mark each time a different region ? if there is
> such an
> >> option, I will really appreciate if u can explain what parameters (file
> >> type ect...) it should contain.
> >>
> >> I really want to come to the tutorial, but the thing is I live in the
> >> other side of the sea:) so that won't be so easy for me to do...
> >>
> >> Thanks again for all your help
> >>  Rotem
>
>
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