Define ROIs for each subject

Submitted by aliasaei on Mon, 05/16/2016 - 20:48

I was wondering if we can define the ROIs for each subject individually in the original structural image space, instead of defining an ROI in the normalized space?

Forums:

YAN Chao-Gan

Tue, 05/17/2016 - 01:20

Yes, you can.

In DPARSFA, there is a button Define ROI Interactively *

aliasaei

Tue, 05/17/2016 - 19:52

Thanks! This option only provides defining sphere ROIs. What about defining mask ROIs in nii format?

YAN Chao-Gan

Wed, 05/18/2016 - 08:37

In "Define ROI":

1. Click + Seed Series

2. Choose a configuration file, e.g., Config.txt

The contents should be:

Seed_Time_Course_List:

/XX/MaskSub1.nii

/XX/MaskSub2.nii

/XX/MaskSub3.nii

 

 

Please make sure the first line is: "Seed_Time_Course_List:".

Best,

Chao-Gan

aliasaei

Wed, 05/18/2016 - 14:46

Thank you for the quick response. We have more than one mask files for each subject and would like to find the correlation between these ROIs.
For example for subject1 we have:
   subject1_mask1.nii
   subject1_mask2.nii
which both are in the t1mpragesag.nii space.
How should be the contests of Config.txt file in that case?

aliasaei

Wed, 05/18/2016 - 19:11

I also tested as you mentioned for just one ROI per subject and I get this error:

Error using DPARSFA_run (line 3893)
Name-value pair arguments must come in pairs.

Error in DPARSFA>pushbuttonRun_Callback (line 1761)
    [Error]=DPARSFA_run(handles.Cfg);


Error in gui_mainfcn (line 95)
        feval(varargin{:});

Error in DPARSFA (line 30)
    gui_mainfcn(gui_State, varargin{:});

YAN Chao-Gan

Thu, 05/19/2016 - 08:42

1. If you have several masks for a subject. I suggest you write a code to call y_SCA.

[FCBrain, Header] = y_SCA(AllVolume, ROIDef, OutputName, MaskData, IsMultipleLabel, IsNeedDetrend, Band, TR, TemporalMask, ScrubbingMethod, ScrubbingTiming, Header, CUTNUMBER)

2. What version of DPARSF/DPABI are you using for this error?

Best,

Chao-Gan

aliasaei

Tue, 05/24/2016 - 13:58

Seems like the output of the Y_SCA is a functional connectivity map for each ROI but we are looking for the correlation matrices.
We are using release V2.0_151201.

YAN Chao-Gan

Tue, 05/24/2016 - 23:20

Hi Ali,

Then you can use y_ExtractROISignal.m

Best,