ROI based analysis of ASL data

[shani...@gmail.com]

Dear Dr. Wang,

My name is Shania Mereen Soman, a Junior Research Fellow currently working on ASL images. We are analysing healthy controls vs MCI and AD. The images were acquired using GE 3T MRI scanner. ASL data pre-procesing steps (Realign, Normalisation, Smoothing) were done using SPM GUI (SPM12 and Matlab 2015b). Then CBF quantification was done using ASLtbx in GUI mode. We got CBF values for the whole brain. But for our study we need CBF ROI values for the specific  regions such as Posterior Cingulate, Precuneus. We have made masks for Posterior cingulate and Precuneus using wfu pick atlas. Can we incorporate this mask to get CBF values of the specified regions or could you please suggest a method to get the desired results.

Thank You very much for your time,

Kind Regards,

Shania Mereen Soman

Junior Research Fellow

Sree Chitra Tirunal Institute of Medical Sciences and Technology

Trivandrum, Kerala, India

[redhatw]

Hi Shania,

    If you have the masks ready and already warped cbf maps into the standard space, you can use the attached extractroidata.m to get the mean ROI CBF values.

Just one note, for GE scanner, you can get the CBF map from the GE workstation. Otherwise you can use ASLtbx to do that too (example scripts can be found in the maillist or I can send).

Ze

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[shani...@gmail.com]

Dear Dr. Wang

Thank you for sending me the scripts. I tried running the script but I didn't get any value. Here I am attaching the screenshot of Matlab command window that showed up after running the script, the smoothed mean cbf image and mask image.

Kindly go through the attached images and help me to get the desired results.

Kind Regards,

Shania

[Sudipto Dolui]

Hi Shania,

You should have a file roicbf.txt where the results have been printed.

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[shani...@gmail.com]

Dear Sudipto,

I didn't get any text file after running the script. I want to know if there is anything wrong with my image. Could you please go through my images and help me to get the desired results.

Kind Regards,

Shania

On Tuesday, February 27, 2018 at 3:35:48 PM UTC+5:30, Sudipto Dolui wrote:

Hi Shania,

You should have a file roicbf.txt where the results have been printed.

On Tue, Feb 27, 2018 at 1:19 PM, <shani...@gmail.com> wrote:

Dear Dr. Wang

Thank you for sending me the scripts. I tried running the script but I didn't get any value. Here I am attaching the screenshot of Matlab command window that showed up after running the script, the smoothed mean cbf image and mask image.

Kindly go through the attached images and help me to get the desired results.

Kind Regards,

Shania

On Friday, February 23, 2018 at 5:12:29 PM UTC+5:30, shani...@gmail.com wrote:

Dear Dr. Wang,

My name is Shania Mereen Soman, a Junior Research Fellow currently working on ASL images. We are analysing healthy controls vs MCI and AD. The images were acquired using GE 3T MRI scanner. ASL data pre-procesing steps (Realign, Normalisation, Smoothing) were done using SPM GUI (SPM12 and Matlab 2015b). Then CBF quantification was done using ASLtbx in GUI mode. We got CBF values for the whole brain. But for our study we need CBF ROI values for the specific  regions such as Posterior Cingulate, Precuneus. We have made masks for Posterior cingulate and Precuneus using wfu pick atlas. Can we incorporate this mask to get CBF values of the specified regions or could you please suggest a method to get the desired results.

Thank You very much for your time,

Kind Regards,

Shania Mereen Soman

Junior Research Fellow

Sree Chitra Tirunal Institute of Medical Sciences and Technology

Trivandrum, Kerala, India

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[Sudipto Dolui]

Hi Shania,

I can't see all the files in the working directory (left side of your image). It only shows up to fitbutter.m and the text file roicbf.txt should be below that since they are arranged in alphabetical order. Just scroll down to see if the file is there. Let me know if you still can't find it.

Best,

Sudipto

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[shani...@gmail.com]

Dear Sudipto,

I tried to show the Matlab command window. After running the script I couldn't see any results or error. The left side of the attached image (matlab command window) is the folder containing ASL scripts. Please let me know if there is any problem with my smoothed cbf map and the 3-D mask.

Kind Regards,

Shania

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[Sudipto Dolui]

Dear Shania,

What I tried to say is that there should be a text file created in your working directory with the relevant ROI values. If the folder with the ASL scripts is your working directory, then the text file has been created over there.

If you want to print your results in the command window, you can try running the attached code. Let me know if it worked.

Sudipto

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[Farhia Saphira]

Dear, dr. Wang, Sudipto, and Shania

I'm Saphira. I'm a radiology student, and I don't have much knowledge in MATLAB. I want to calculate CBF value using ROI in specific region like in stroke or tumor. 

After I draw VOI file in the mean CBF file, I put the get_meanroidat.m file to my ASLTBX directory, and running it in my matlab. I choose my VOI file and choose mean CBF file as the source file. But I got this error result in my MATLAB, can you please let me know what the problem and how to solve it? 

Thank you.

Best regard, 

Saphira

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[Sudipto Dolui]

How are you creating the VOI? Instead of saving in .voi format, try saving in .nii format and check if it solves the problem. 

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[Ze Wang]

I attached the code here.

We are planning to update the manual and the package to make it more user friendly. We will provide more tutorials too.  

Ze

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