[Mristudio-users] automate DTIstudio processing

Wed Aug 7 18:44:25 EDT 2013

I found that I can easily make mistake in the BinaryMap text file.
Start from just one ROI to get yourself familiarized.

On Wed, Aug 7, 2013 at 11:40 AM, Dorian P. <alb.net at gmail.com> wrote:

> Try adding FiberColor and ColorMode. Also make sure the sizes of the image
> correspond. Below is an example that works for me.
>
>
> *** ROI Map ***
>
> Begin
>  ImageWidth: 181
> ImageHeight: 217
>  ImageSlices: 181
>
> PixelSizeWidth: 1.000000
>  PixelSizeHeight: 1.000000
> SliceThickness: 1.000000
>
> SliceOrientation: 1
> SliceSequencing: 0
>
>     BinaryFile: C:\temp\OR.dat
> Operation: 0
>  FiberColor: (255,0,0)
> ColorMode: 0
>
>     BinaryFile: C:\temp\AND_#1.dat
> Operation: 1
>  FiberColor: (255,0,0)
> ColorMode: 0
>
>     BinaryFile: C:\temp\NOT.dat
> Operation: 3
>  FiberColor: (255,0,0)
> ColorMode: 0
>
> End
>
> Note:
> Slice Orientation: 0=Coronal, 1=Axial, 2=Sagittal
> Slice Sequencing: 0=Positive, 1=Negative
>
> *** ROI Map ***
>
>
>
> 2013/8/7 Youngmin Huh <ymin1123 at gmail.com>
>
>> I edited map file generated by ROIEditor as below.
>> There are two ROIs with 'or(0)' operation for the first one, and
>> 'and(1)' operation for the second one.
>> -----------------------------------------------------
>> *** ROI Map ***
>>
>> Begin
>>         ImageWidth:     240
>>         ImageHeight:    240
>>         ImageSlices:    152
>>
>>         PixelSizeWidth: 1.000000
>>         PixelSizeHeight:        1.000000
>>         SliceThickness: 1.000000
>>
>>         SliceOrientation:       1
>>         SliceSequencing:        0
>>
>>         BinaryFile:
>> E:\data\isotropic_data\ADHD\72804182\DTIstudio\test_AAL\ROImask\Amygdala_L_b.dat
>>         Operation:      0
>>
>>         BinaryFile:
>> E:\data\isotropic_data\ADHD\72804182\DTIstudio\test_AAL\ROImask\Amygdala_R_b.dat
>>         Operation:      1
>>
>> End
>>
>> Note:
>>         Slice Orientation: 0=Coronal, 1=Axial, 2=Sagittal
>>         Slice Sequencing:  0=Positive, 1=Negative
>>         ROI Operation:  0=OR, 1=AND, 3=NOT
>>
>> *** ROI Map ***
>> -----------------------------------------------------
>>
>> And I load map file as Binary map format on DTI studio, but nothing
>> happened.
>> I can load the map file on ROIEditor, but can't load at DTI studio. I
>> wonder why.
>>
>> Thanks,
>>
>> YM Huh
>>
>>
>> 2013/8/7 susumu mori <smoriw at gmail.com>:
>> > Hi YM,
>> >
>> > Did you open the ROI files as BinaryMap format?
>> > Once you save BinaryMap by RoiEditor, you have to edit the saved text
>> file
>> > and specify how you want to combine the multiple ROI files using
>> AND/OR/NOT
>> > operations.
>> >
>> >
>> > On Tue, Aug 6, 2013 at 10:29 PM, Youngmin Huh <ymin1123 at gmail.com>
>> wrote:
>> >>
>> >> Thanks for your comment!
>> >> I'm using ROIs for fiber tracking.
>> >>
>> >> I used ROIeditor to generate binay map files, and changed
>> >> ROIMap_map.dat to ROIMap_map.map.
>> >> It worked! I can load multiple RoIs at ROIEditor, but I can't figure
>> >> out how I could load it on DTI studio.
>> >> I tried to load map file using the "load" icon in "Fiber" tab,
>> >> "ROI-Operation" section, but nothing happened.
>> >> Of course I finished whole brain fiber tracking before I load ROIs.
>> >> How could I find fibers connecting ROIs with my map file on DTI studio?
>> >>
>> >> Thanks,
>> >>
>> >> YM Huh
>> >>
>> >> 2013/8/7 susumu mori <smoriw at gmail.com>:
>> >> > Are you using ROIs for image quantification or fiber tracking?
>> >> > From the second question, I guess you want to do a comprehensive
>> fiber
>> >> > tracking with a lot of ROIs.
>> >> > If that is the case, Yajing is the right person to ask.
>> >> > We do have command line-version of the tracking.
>> >> >
>> >> > Also, please take a look at RoiEditor at www.mristudio.org. It
>> manages
>> >> > multiple ROIs much better.
>> >> > You can find some tips in the FAQ section.
>> >> >
>> >> >
>> >> > On Tue, Aug 6, 2013 at 5:01 AM, Youngmin Huh <ymin1123 at gmail.com>
>> wrote:
>> >> >>
>> >> >> Hi, I'm a new user.
>> >> >> I have been struggling with DTIstudio for few weeks.
>> >> >> I have some questions to ask.
>> >> >>
>> >> >> 1) how can I define multiple ROIs?
>> >> >> I drew two ROIs with "ROI drawing" on "ROi" tab, and saved them into
>> >> >> "binary maps".
>> >> >> But It generated 3 dat files, but no map file (ROIMap_00.dat,
>> >> >> ROIMap_01.dat, ROIMap_map.dat).
>> >> >> I tried again with ROI editor, but It didn't work either. It
>> generated
>> >> >> only dat files.
>> >> >> How can I generate .map file to load ROIs?
>> >> >>
>> >> >> 2) Is there any way to automate DTI processing?
>> >> >> I'm going to use 116 ROI masks to obtain whole brain connectivity.
>> >> >> It seems like hard work to do all this process manually.
>> >> >>
>> >> >> Any comment would be appreciate.
>> >> >>
>> >> >> Thanks,
>> >> >>
>> >> >> YM Huh
>> >> >> _______________________________________________
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>> >> >
>> >> >
>> >> >
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