To get ROI data

[박강민]

Hello.

Dear Sir,

I alredy read the method for getting the ROI data from ASL in the discussion board.

We can get it with normalized CBF map, ROI mask, and extractroidata.m file, which you already uploaded in the discussion board.

I wonder that what is the normalized CBP map?

Is it the file of meanCBF.nii (the resulting file of the ASLtbx in GUI mode)? 

Thank you for your help.

Sincerely yours,

Kang Min, South Korea.

[Sudipto Dolui]

The normalized CBF map will be the map in the MNI space and won't be meanCBF.nii.

Sudipto

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[박강민]

Dear Sudipto, 

Thank you for our response. 

How can I get the normalized CBF map in the MNI?

Is it the result of the ASLtbx in the GUI mode? 

Thank you for your help. 

Sincerely yours, 

Kang Min Park, MD.

2020년 11월 14일 토요일 오전 3시 8분 34초 UTC+9에 sudipt...@gmail.com님이 작성:

[Sudipto Dolui]

Dear Kang Ming,

I didn't use the GUI, so don't know if that produces the normalized images. Ze will be able to answer that. 

Do you have any image with prefix w or sw? Those can be the normalized images. But even before that, note that your image and ROIs should be in the same space. So if your ROI is in the MNI space, then only you need the CBF images in the MNI space. On the other hand, if your ROIs are in the ASL or T1 space, you need to use the CBF images in the corresponding space.

Sudipto

To view this discussion on the web visit https://groups.google.com/d/msgid/asltbx-discussion-board/30bf7cce-c697-4abf-9865-01ad27d1c12cn%40googlegroups.com.

[박강민]

Dear Sudipto, 

Thank you for your response. 

I only used the ASLtbx GUI mode and extractroidata.m file. 

I wonder that 

"extractroidata.m file can be applied after the ASLtbx GUI mode for calculation of CBF map?" or "After downloading the ASL files from MRI, we can do normalization the files with SPM. Then,  extractroidata.m file can be applied without calculation of CBF map with the ASLtbx GUI mode?" 

Thank you. 

Sincerely yours, 

Kang Min. 

2020년 11월 14일 토요일 오후 12시 25분 21초 UTC+9에 sudipt...@gmail.com님이 작성:

[redhatw]

Pls see my comments below marked with ">>"

On Sat, Nov 14, 2020 at 8:49 PM 박강민 <smile...@gmail.com> wrote:

Dear Sudipto, 

Thank you for your response. 

I only used the ASLtbx GUI mode and extractroidata.m file. 

I wonder that 

"extractroidata.m file can be applied after the ASLtbx GUI mode for calculation of CBF map?" or "After downloading the ASL files from MRI, we can do normalization the files with SPM. Then,  extractroidata.m file can be applied without calculation of CBF map with the ASLtbx GUI mode?" 

>>> after CBF calculation, you should normalize the mean CBF map (ideally you should run outlier cleaning after you calculate the CBF map image series and then get the cleaned mean CBF map. You can refer to the example of "outlier cleaning" given in the webpage for how to do outlier cleaning using scripts) to the MNI space. you can then run extractroidata.m to get CBF value in each of the AAL ROIs or ROIs you provided.

To view this discussion on the web visit https://groups.google.com/d/msgid/asltbx-discussion-board/d715e7bf-b4de-401c-b26b-f943b454fafbn%40googlegroups.com.

--

Ze Wang, PhD

[박강민]

Thank you for your help.

2020년 11월 29일 일요일 오전 1시 23분 38초 UTC+9에 red...@gmail.com님이 작성:

[Farhia Saphira]

Hi, Dr Ze Wang.

I want to ask, in the previous email, you mentioned that we have to normalize cleaned mean CBF map by running outer cleaning. You also mentioned that the manual using scripts is given in the webpage. Could you give me the webpage that mention instruction to do this?. I've been looking for manuals, but haven't figure it out.

Thank you so much for you kindness.

Best,

Saphira.

[tianci_369358727]

这是一封自动回复邮件。已经收到您的来信，我会尽快回复。

[Ze Wang]

Hi Saphira,

     You can take a look at the example code and customized code in the following share drive. You will find outlier cleaning code in a file named "batch_run_outlierclean.m" or "batch_outlier_clean.m". After you register the outlier cleaned CBF maps to the MNI space, you can use the toycode "extractroidata.m" to extract mean CBF from the atlas ROI images you will select.  

https://somumaryland-my.sharepoint.com/:f:/g/personal/ze_wang_som_umaryland_edu/EuMRw4t_D_FEjN91um9h5ZABjTG0t0lmRNTFwJ8D_gXs_Q?e=hW7M4U

To view this discussion on the web visit https://groups.google.com/d/msgid/asltbx-discussion-board/a2b6b89e-d365-462b-a034-ad149bf388f9n%40googlegroups.com.

[tianci_369358727]

这是一封自动回复邮件。已经收到您的来信，我会尽快回复。