[Mristudio-users] automate DTIstudio processing
Youngmin Huh
ymin1123 at gmail.com
Thu Aug 8 02:40:08 EDT 2013
Thanks a lot!
I made map file with one ROI and added FiberColor and ColorMode.
And than I tried with two ROIs, and It worked!
I have one more question.
my ROIs were nii files, so I converted it into dat file using diffeoMap.
(saved a nii file into a raw image on DTIstudio, and converted the RAW
file's filetype to "byte" on DiffeoMap.)
I want to automate this process using a command line, I wonder If it's possible.
I heard that DTI studio could do that. Does DiffeoMap also have such
function in it?
If It does, should I download a new command line program for it?
Thanks,
YM Huh.
2013/8/8 susumu mori <smoriw at gmail.com>:
> 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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