[Mristudio-users] test-retest

[susumu mori]

If you are using RoiEditor to define ROIs, you can directly save them
as the Analyze format.
If you are using DtiStudio, you can save the ROI as a binary or binary
map format. You can read them as image files and save them as Analyze.

On Thu, Apr 7, 2011 at 7:56 AM, Miguel Burgaleta
<miguel.burgaleta at uam.es> wrote:
>
> 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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