[Mristudio-users] Overplus

[Ayo Owegi]

Hi. Would you kindly remove me from this mailing list? Thanks !

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> On Aug 27, 2014, at 2:36 PM, Susumu Mori <smoriw at gmail.com> wrote:
> 
> Hi Prachi,
> 
> Unfortunately, we have not yet confirmed the validity of the gradient table orientation of the Philips Overplus data.
> The complexity arises from the fact that such data could be loaded as; 
> 1) raw data and gradient table supplied manually to the gradient table window
> 2) Enhanced DICOM data with automated table reader
> 3) PAR file with automated table reader
> 
> In each method, the gradient table may be stored in different coordinate system.
> What we know is #1 works but in this case, you need to use Jon Farrel's gradient table calculation software, which can be downloaded from F.M. Kirby Center website.
> 
> Hangyi has several experience with #2 and #3, but we are not offering "official" solutions for these data.
> Our recommendation is always, "DO NOT USE OVERPLUS", but I guess it won't help you.
> 
> In general, I would assume the gradient table recalculation option needs to be checked for #2 and #3.
> In any case, users should take a self-defense measure. One good way is to get an image with a severe oblique angle rotation, while the brain is more or less upright. In this way, the brain should be tilted in the image. If the color map shows right-left symmetric (the color map looks fine), then the gradient table needs to be rotated (the check box needs to be checked). If the gradient table is pre-rotated, the color should be asymmetric (because the brain is tiled in the image) and no need to check the gradient table rotation checkbox.
> 
> 
>> On Wed, Aug 27, 2014 at 1:41 PM, Prachi Dubey <pxd2010 at gmail.com> wrote:
>> Hi All,
>> Has anyone had issues with gradient overplus on option with the Philips Data. I have Philips dataset, with Overplus on and the rotate gradient option should be checked for this datset. However, fiber tracking is not accurate with the rotate option checked on. It is accurate without the option.
>>  
>> Anyone faced this issue.
>>  
>> Prachi
>>  
>>> On Tue, Aug 26, 2014 at 11:50 AM, Susumu Mori <smoriw at gmail.com> wrote:
>>> Hi Amit,
>>> 
>>> The Talairach template is usually used to a rough estimation of the brain coordinates and, in my understanding, rarely used as a target of volume measurements.
>>> I must admit that we haven't used this template for volume measurements either.
>>> 
>>> I would recommend you to use our MNI templates such as JHU-ss (single-subject).
>>> 
>>> We are about to release an entirely new pipeline for T1/DTI segmentation based on a multi-atlas approach. I hope this will be a better solution for you in the near future.
>>> 
>>> 
>>>> On Mon, Aug 25, 2014 at 9:11 AM, Amit Wani <amitwani111 at gmail.com> wrote:
>>>> Dear Experts,
>>>> 
>>>> I am trying to calculate volumes of some structures (hippocampus, cingulum etc) in T1 anatomical images. I used JHU Talairach template (1x1x1 mm3) available in ROIEditor as my reference image for analysis. I saved the predefined ROIs for the structures as well.
>>>> 
>>>> But when i calculated the volumes of these ROIs, they look little higher. For example, for right side of hippocampus, number of voxels are 5901 (i.e., volume 5.9 cm3). But in literature, the volumes are in the range of 2.5 - 3 cm3. Why is this difference?
>>>> 
>>>> Thank you,
>>>> Amit.
>>>> 
>>>> 
>>>> 
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