[Mristudio-users] IFO, MdLF and EmC

[Andreas Horn]

Dear Yajing,

thank you so much for your time to copy out the links for me. Unfortunately, I now realized that I had tried to use these tracts before and they don't seem to work with our software. Probably they only are to be displayed by your software bundle dtistudio/roieditor.

If I try to display them with SPM/Mricron, etc. they seem misplaced/shifted somehow (see picture).
Somehow they don't seem to be normalized into ICBM-Space or our software doesn't understand the normalization somehow - which is weird because e.g. the dti-81 atlas of the LONI-Institute works fine.

As an example, this is how SPM/mricron displays the left SLF-FT of your atlas.


Probably you don't have a solution for this coregistration-issue by hand and I completely understand if you don't have the time to go into it.

But I just thought that it could be worth it that you know about the issue.

Thank you so much in any case,

yours sincerely, Andreas


Am 23.07.2011 um 17:22 schrieb Yajing Zhang:

> Hi, Andreas
> 
> You can find the fiber atlas in: http://lbam.med.jhmi.edu/cmrm/Data_Yajing/fiberMenu.htm
> The components of SLF can be downloaded in: http://lbam.med.jhmi.edu/cmrm/Data_Yajing/longAssociation.htm
> The corresponding paper is: "Atlas-guided tract reconstruction for automated and comprehensive examination of the white matter anatomy." Neuroimage 52(4):1289-1301 (2010). 
> 
> 
> Best regards,
> Yajing
> 
> 
> 
> On Fri, Jul 22, 2011 at 7:44 PM, susumu mori <susumu at mri.jhu.edu> wrote:
> Hi Andreas,
> 
> With 2-2.5mm resolution, the external and extreme capsules are difficult to separate, but I agree that IFO seems to occupy a good portion of these structures.
> 
> As for the different sections of the SLF, please refer to Yajing Zhang's paper in NeuroImage about the automated tractography. She created probabilistic maps of the different sections of the SLF in our atlas, which are available for download. Please contact Yajing about the location of the files. They may be already included in RoiEditor but I need to ask Xin.
> 
> MdLF is currently not defined in our atlas.
> 
> Susumu
> 
> On Fri, Jul 22, 2011 at 10:58 AM, Andreas Horn <mail at andreas-horn.de> wrote:
> Hello everybody, dear Susumu,
> 
> I have read your response about IFO and SFO (http://lists.mristudio.org/pipermail/mristudio-users/2011/001928.html).
> 
> Now I still wonder what anatomical structures are most likely included (or with which ones the cut-set is biggest) in IFO.
> When I look at the tract, it seems that the extreme capsule is definitely included, most likely also parts of external capsule, possibly uncinatus. Is this correct?
> 
> I would also be very glad about three-dimensional data of the MdLF as delineated in Makris 2009 and/or the partialized SLF (I-III plus AF) but can't seem to find them anywhere. Do you have any ideas how to get access to these files?
> 
> All I want to do is to assign our tracts to anatomical structures.
> 
> Thank you so much for your help!
> 
> Yours, sincerely, Andreas Horn
> 
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