registration command line

[imwh...@gmail.com]

Dear Dr.Yeh,

Hello. I am having problems in registration. Using GUI, I can registrate the AAL template to DTI space, but now I want to do the batch processing. How can I use the command line? Does it need many steps? Cause when using fsl, it is quite complicated.

Thank you for taking your time to read this.

Yours,

Zoe Wang

[Fang-Cheng Yeh]

Hi Zeo,

    Here's the instructions: http://dsi-studio.labsolver.org/Manual/command-line-for-dsi-studio#TOC-Rigid-body-rotation-and-spatial-normalization

    If there is anything not working expectedly, please let me know. I will fix it.

Best,

Frank

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[imwh...@gmail.com]

Thanks for replying, Dr. Yeh.

But there is still a problem. Can I use the intermediate affine matrix in the registration? Because I want to get an AAL template in specific diffusion space, first I need to get the affine matrix of registering DTI to MNI space. Then I need to do the matrix reverse to map AAL in MNI to DTI space. So can I do this process using DSIStudio?

Thanks.

Zoe

在 2020年10月20日星期二 UTC+8下午9:10:30，imwh...@gmail.com写道：

[Fang-Cheng Yeh]

Hi Zoe,

    Sorry I am not very sure about the question here. You may check out the documentation and see if the command line functions work for you.

Best regards,

Frank

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[imwh...@gmail.com]

Dear Dr. Yeh,

Thanks for the help!

Best regards,

Zoe

在 2020年10月23日星期五 UTC+8上午11:04:33，Frank Yeh写道：

Hi Zoe,

    Sorry I am not very sure about the question here. You may check out the documentation and see if the command line functions work for you.

Best regards,

Frank

On Wed, Oct 21, 2020 at 9:33 AM <imwh...@gmail.com> wrote:

Thanks for replying, Dr. Yeh.

But there is still a problem. Can I use the intermediate affine matrix in the registration? Because I want to get an AAL template in specific diffusion space, first I need to get the affine matrix of registering DTI to MNI space. Then I need to do the matrix reverse to map AAL in MNI to DTI space. So can I do this process using DSIStudio?

Thanks.

Zoe

在 2020年10月20日星期二 UTC+8下午9:10:30，imwh...@gmail.com写道：

Dear Dr.Yeh,

Hello. I am having problems in registration. Using GUI, I can registrate the AAL template to DTI space, but now I want to do the batch processing. How can I use the command line? Does it need many steps? Cause when using fsl, it is quite complicated.

Thank you for taking your time to read this.

Yours,

Zoe Wang

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[imwh...@gmail.com]

Hi, Dr.Yeh,

Sorry to bother again.

To clearly express my problem, I tried to upload an image but didn't make it. And the problem is if there is a command line, which can replace the operation in DSIStudio->StepT3 FiberTracking->Regions->open MNI region. When I use this operation in GUI,it will do the registration automatically. I hope I've made it clear.

Thanks very much.

 

Best regards,

Zoe

在 2020年10月23日星期五 UTC+8上午11:04:33，Frank Yeh写道：

Hi Zoe,

    Sorry I am not very sure about the question here. You may check out the documentation and see if the command line functions work for you.

Best regards,

Frank

On Wed, Oct 21, 2020 at 9:33 AM <imwh...@gmail.com> wrote:

Thanks for replying, Dr. Yeh.

But there is still a problem. Can I use the intermediate affine matrix in the registration? Because I want to get an AAL template in specific diffusion space, first I need to get the affine matrix of registering DTI to MNI space. Then I need to do the matrix reverse to map AAL in MNI to DTI space. So can I do this process using DSIStudio?

Thanks.

Zoe

在 2020年10月20日星期二 UTC+8下午9:10:30，imwh...@gmail.com写道：

Dear Dr.Yeh,

Hello. I am having problems in registration. Using GUI, I can registrate the AAL template to DTI space, but now I want to do the batch processing. How can I use the command line? Does it need many steps? Cause when using fsl, it is quite complicated.

Thank you for taking your time to read this.

Yours,

Zoe Wang

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[L. Tanushree]

Dear Frank,

Is there any suggestion to run AAL atlas for tractography for batch processing? I went through the forum and saw that the solutions to the same problem was not provided. Does this mean that the problem of batch processing with AAL atlas  cannot be done.

If yes, could you kindly provide an informative solution

Regards

Tanu

[Frank Yeh]

Hi Tanu,

You may need to copy the AAL atlas to the atlas folder in DSI
Studio, as per instructions at
https://dsi-studio.labsolver.org/doc/gui_t3_roi_tracking.html

However, AAL does not align with ICBM152 2009, and there will be
very obvious misalignment error.

Best regards,
Frank

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[L. Tanushree]

Thank you for your response. Is there a way to do the following steps of individual analysis using command in Batch code?
Step T3 <selecting .fib file<Regions - open MNI Region <selecting AAL.nii < Fiber tractography<connectivity matrix

L. Tanushree
Junior Research Fellow
Department of NI&IR
National Institute of Mental Health and Neuroscience
Bengaluru- 560029

[Frank Yeh]

dsi_studio --action=trk --source=subject001.fib.gz
--fiber_count=10000000 --output=no_file
--connectivity=/some_folder/AAL_mni.nii.gz --connectivity_value=count

Make sure to include 'mni' in the file name so that DSI Studio will
treat it as MNI regions.

On Tue, Oct 8, 2024 at 10:34 AM L. Tanushree

[Frank Yeh]

Sorry I won't be able to fix your code for you.

If there is a bug in DSI Studio , we will fix it.

You may need to test each command and check the log output to see if there is a problem in your code.

Best

Frank

I have tried adding atlas and renaming the atlas file but the code did not work. The code creates src and fib files but I need a connectivity matrix of count, FA and MD. I tried to get the connectivity matrix but the file created is txt. Can you please check the code? Please let me know.

L. Tanushree
Junior Research Fellow
Department of NI&IR
National Institute of Mental Health and Neuroscience
Bengaluru- 560029

[L. Tanushree]

I totally agree with you but the command gives a connectivity text file which I can't use can you please help me to solve that issue.

L. Tanushree
Junior Research Fellow
Department of NI&IR
National Institute of Mental Health and Neuroscience
Bengaluru- 560029

[Frank Yeh]

I did take a quick look at your code, and some of the command lines
called in the code do not follow the document and example on the
website.
If there is an issue in DSI Studio, you may also need to post the
exact command used and its log output.

I am willing to help if there is a glitch in DSI Studio and I cannot

fix your code for you.

I am sorry about that.
Frank

On Thu, Oct 24, 2024 at 11:58 AM L. Tanushree

[L. Tanushree]

Thanks for your guidance.

L. Tanushree
Junior Research Fellow
Department of NI&IR
National Institute of Mental Health and Neuroscience
Bengaluru- 560029