[Mristudio-users] test-retest

[Miguel Burgaleta]

Hi Susumu,

Is there any way to save ROIs in analyze format? If not, can we  
somehow convert dat files into analyze or nifti images within DTIStudio?

Thanks
Miguel



On Apr 2, 2011, at 8:54 PM, susumu mori wrote:

> Please see below;
>
> On Fri, Apr 1, 2011 at 4:39 AM, Miguel Burgaleta
> <miguel.burgaleta at uam.es> wrote:
>>
>> Hi Susumu,
>>
>> Thanks for your reply.
>>
>> I find your suggestion very helpful! However, with that method I  
>> don't
>> see how to separate the reproducibility of the tract from the rater
>> reliability. If the tract in time 1 is different from that in time 2,
>> we don't really know to what extent it is caused by small errors in
>> the ROI placement, or by problems of reproducibility...
>>
>> Another possibility would be to do tractography in time 1 twice, and
>> once in time 2, so that we can look at the time1-time2  
>> reproducibility
>> relative to the time1-time1 reliability.
>
> Yes, for intra/inter-operator reproducibility, you have to pick one
> data (e.g. Time 1) and perform ROI drawing multiple times by the same
> and different operators.
>
> For inter-measurement reproducibility, you have to have Time 1 and
> Time 2 data. In this case, if you draw ROI independently on Time 1 and
> 2, you have both inter-measurement and intra-operator reproducibility
> mixed.
>
>>
>> Also, can ROIs be transformed with Diffeomap as well (just like I
>> suggested in my previous email)? That would help ensure that
>> differences are due to reproducibility only.
>>
>
> To remove the intra-operator factor from the inter-measurement
> reproducibility, you can transform the ROI used for Time 1 to Time 2.
> In this case, I suggest you to save the ROIs as the "Binary Map"
> format. For example, suppose you drew 3 ROIs for tractography on Time
> 1. If you save the ROIs as the Binary Map, you'll get 4 files. Three
> files are 1/0 binary mask files for 3 ROIs. The final one is a header
> file in a text format. You can read and study the header. There is an
> explanation section at the bottom of the header file.
>
> Then you can apply the transformation matrix to the 3 ROI files in
> DiffeoMap. As mentioned in the earlier email, you can use, for
> example, b0 (Time1) to b0 (Time2) linear transformation and save the
> transformation matrix. This matrix can be applied to the 3 ROI files.
> Save these 3 new transformed ROI files. Then, rewrite the text header
> files and specify the filenames of the 3 new ROI files.
>
> You can load all necessary files (vector and FA files) for Time 2 for
> tractography in DtiStudio. Then, you can load the revised Binary Map,
> which will load the 3 new ROI files and apply the ROIs.
>
> Hope this will do.
>
> Susumu
>
>
>> Thanks,
>> Miguel
>>
>>
>> On Apr 1, 2011, at 12:15 AM, susumu mori wrote:
>>
>>> Hi Miguel,
>>>
>>> You can do it using Diffeomap (or FSL or SPM). First do tractography
>>> in image 1 and 2 independently. Save the results as a 3D 1/0 mask in
>>> DtiStudio.
>>> Then run a rigid transformation between the image 1 and 2. You can  
>>> do
>>> FA vs FA but b0 vs b0 could be easier because FA maps could have  
>>> some
>>> random intense pixels outside the brain that may interfere with the
>>> rigid alignment. Save the transformation matrix and apply it to your
>>> 1/0 binary fiber mask image. Then you can superimpose the aligned #1
>>> and original #2 see the reproducibility. You can do all these very
>>> easily by DiffeoMap.
>>>
>>> Susumu
>>>
>>> On Wed, Mar 30, 2011 at 12:56 PM, Miguel Burgaleta
>>> <miguel.burgaleta at uam.es> wrote:
>>>>
>>>> Hi,
>>>>
>>>> We have a sample of DWI acquired twice for each subject, 1 month in
>>>> between, and would like to analyze the test-retest  
>>>> reproducibility of
>>>> a selection of tracts with DTIStudio. We would also like to see the
>>>> effect of outlier pixel rejection on the reproducibility.  
>>>> However, we
>>>> are not sure of how to proceed so that we control for the intra- 
>>>> rater
>>>> reliability.
>>>>
>>>> One option we thought of is to perform tractography at time 1, save
>>>> both binary tracts and ROIs, and then register each FA image in
>>>> time 1
>>>> to its corresponding FA image in time 2, apply that  
>>>> transformation to
>>>> the ROIs and get the tract for time 2. Is this feasible with
>>>> DTIStudio?
>>>>
>>>> If you know a better way to do this, please let me know.
>>>>
>>>> Best,
>>>> Miguel
>>>>
>>>>
>>>>
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