[Mristudio-users] automate DTIstudio processing
Youngmin Huh
ymin1123 at gmail.com
Thu Aug 8 09:41:32 EDT 2013
If there is no such service,is it possible to make a script to perform
repeated operation?
I do not have good computer skills.
Can you give me some demo or hint for it?
I would really appreciate it.
Thanks,
YM Huh
2013/8/8 Youngmin Huh <ymin1123 at gmail.com>:
> If there is no such service,is it possible to make a script to perform
> repeated operation?
> I do not have good computer skills.
> Can you give me some demo or hint for it?
> I would really appreciate it.
>
> Thanks,
>
> YM Huh
>
>
> 2013/8/8 Hangyi Jiang <hjiang at jhmi.edu>:
>> sorry, right now, we don't have such service (command line, batch mode pipeline processing ) for general users.
>>
>> best,
>>
>> hangyi
>>
>> ________________________________________
>> From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of Youngmin Huh [ymin1123 at gmail.com]
>> Sent: Thursday, August 08, 2013 2:40 AM
>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
>> Subject: Re: [Mristudio-users] automate DTIstudio processing
>>
>> 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
>>>>> >> >> _______________________________________________
>>>>> >> >> mristudio-users mailing list
>>>>> >> >> mristudio-users at mristudio.org
>>>>> >> >> http://lists.mristudio.org/mailman/listinfo/
>>>>> >> >> Unsubscribe, send a blank email to:
>>>>> >> >> mristudio-users-unsubscribe at mristudio.org
>>>>> >> >
>>>>> >> >
>>>>> >> >
>>>>> >> > _______________________________________________
>>>>> >> > mristudio-users mailing list
>>>>> >> > mristudio-users at mristudio.org
>>>>> >> > http://lists.mristudio.org/mailman/listinfo/
>>>>> >> > Unsubscribe, send a blank email to:
>>>>> >> > mristudio-users-unsubscribe at mristudio.org
>>>>> >> >
>>>>> >> _______________________________________________
>>>>> >> mristudio-users mailing list
>>>>> >> mristudio-users at mristudio.org
>>>>> >> http://lists.mristudio.org/mailman/listinfo/
>>>>> >> Unsubscribe, send a blank email to:
>>>>> >> mristudio-users-unsubscribe at mristudio.org
>>>>> >
>>>>> >
>>>>> _______________________________________________
>>>>> mristudio-users mailing list
>>>>> mristudio-users at mristudio.org
>>>>> http://lists.mristudio.org/mailman/listinfo/
>>>>> Unsubscribe, send a blank email to:
>>>>> mristudio-users-unsubscribe at mristudio.org
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> mristudio-users mailing list
>>>> mristudio-users at mristudio.org
>>>> http://lists.mristudio.org/mailman/listinfo/
>>>> Unsubscribe, send a blank email to:
>>>> mristudio-users-unsubscribe at mristudio.org
>>>>
>>>
>>>
>>> _______________________________________________
>>> mristudio-users mailing list
>>> mristudio-users at mristudio.org
>>> http://lists.mristudio.org/mailman/listinfo/
>>> Unsubscribe, send a blank email to:
>>> mristudio-users-unsubscribe at mristudio.org
>>>
>> _______________________________________________
>> mristudio-users mailing list
>> mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org
More information about the mristudio-users
mailing list