[Mristudio-users] automate DTIstudio processing

[Dorian P.]

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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> >> >
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