ALFF/fALFF/ReHo using DPARSF

Submitted by FaezeVedaei on Sat, 05/09/2020 - 20:27

Hi 

I have a trouble uploading the data direcoty on DPARSF for doing some processing. Even though I watch the course, I could not get why I can not upload the direcoty and have the list of subject's folder in the assigned window. 

At this time I have all preprocessed rsfMRI data and just want to get ALFF/fALFF/ReHO stuff. 

Can you please let me know first of all if I can you DPARSF for just this purpose with not doing preprocessing and just ALFF/FALFF/ReHo stuff?

Also, can you please clarify me how I have to arrange or upload the input data directory? 

In advanve I appreciate your help.

Thanks

Faeze

Forums:

YAN Chao-Gan

Mon, 05/18/2020 - 00:47

1. Yes, you can.

2. You need to set starting directory name to let DPARSF read the participants ID. 

I suggest you run DPARSF once with the demo data to learn the directory structure needed.

FaezeVedaei

Mon, 05/18/2020 - 22:28

Dr. Chao-Gan
 
Thank you for your response. Yes, finally I could organize data in sub-direcoties and set the naming. But now I got another error during running the preprocessing as I copied here. Can you please check it and let me know how to fix this? Thank you very much
 
 
Regards
Faeze
 
 
 
------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Realign: Estimate & Reslice'
 
SPM12: spm_realign (v7141)                         17:07:58 - 18/05/2020
========================================================================
Completed                               :          17:09:04 - 18/05/2020
 
SPM12: spm_reslice (v7141)                         17:09:04 - 18/05/2020
========================================================================
Completed                               :          17:10:21 - 18/05/2020
Done    'Realign: Estimate & Reslice'
Done
 
Realign Setup:sub_005 OK
 
 
------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Realign: Estimate & Reslice'
 
SPM12: spm_realign (v7141)                         17:10:21 - 18/05/2020
========================================================================
Completed                               :          17:11:24 - 18/05/2020
 
SPM12: spm_reslice (v7141)                         17:11:24 - 18/05/2020
========================================================================
Completed                               :          17:12:38 - 18/05/2020
Done    'Realign: Estimate & Reslice'
Done
 
Moving Head Motion Corrected Files:sub_005 OKMoving Head Motion Corrected Files:sub_004 OKMoving Head Motion Corrected Files:sub_003 OKMoving Head Motion Corrected Files:sub_002 OKMoving Head Motion Corrected Files:sub_001 OK
Reorienting T1 Image Interactively for sub_001: 
Reference to non-existent field 'ReorientMat'.
 
Error in DPARSFA_run (line 1237)
        mat=y_spm_image_Parameters.ReorientMat;
 
Error in DPARSFA>pushbuttonRun_Callback (line 1845)
    [Error]=DPARSFA_run(handles.Cfg);
 
Error in gui_mainfcn (line 95)
        feval(varargin{:});
 
Error in DPARSFA (line 30)
    gui_mainfcn(gui_State, varargin{:});
 
Error while evaluating UIControl Callback.

YAN Chao-Gan

Tue, 05/26/2020 - 01:26

You need to learn from the course how to "reorient" the images (or skip this step). You can not directly hit "X" to close that window.

FaezeVedaei

Wed, 06/10/2020 - 00:50

Hi Dr. Chao-Gan

Thank you for your help you have provided by the tutorial. I watched the video of the tutorial and followed your instruction and that was very helpful in my understanding to doing the steps of analysis. 

I just ran one time practice of doing alff/reho calculation using dpabi. I did the first steps, reorientation and using the first .mat file I created I tried to do other calculation but I do not know for some reason I got the error message in the middle of the process that I copied here. Can you please take a look at and help me how I should resolve this? I really appreciate it.

 

Regards

Faeze

 
Error using DPARSFA_run (line 2700)
Unable to read file
'/Users/mahdi.alizadeh/Desktop/DPABI/Funraw/RealignParameter/sub_005/rp_asub_005.txtrp_rasub_005.txt'. No such file or
directory.
 
Error in DPARSFA>pushbuttonRun_Callback (line 1845)
    [Error]=DPARSFA_run(handles.Cfg);
 
Error in gui_mainfcn (line 95)
        feval(varargin{:});
 
Error in DPARSFA (line 30)
    gui_mainfcn(gui_State, varargin{:});
 
Error while evaluating UIControl Callback.
 

YAN Chao-Gan

Thu, 06/11/2020 - 09:32

Working Dir should be /Users/mahdi.alizadeh/Desktop/DPABI/ other than /Users/mahdi.alizadeh/Desktop/DPABI/Funraw/

FaezeVedaei

Thu, 06/11/2020 - 17:22

Dr. Chao

 

Thank you for the response. But I think the working directory I chose for the calculations (/Users/mahdi.alizadeh/Desktop/DPABI/Funraw) is the same as you chose 'ProcessingAfterRealignment' in your tutorial video. They both have 'FunImgAR' inside.

So, do you still think that I have to choose DPABI rather than Funraw as the main directory?

Can you please clarify me a bit more about this trick of choosing folers and .mat file for calculation after re-alignment? 

Thank you very much.

 

Faeze

FaezeVedaei

Thu, 06/11/2020 - 20:15

Dr. Chao

 

I could finally redo the process and get results. The issue resolved. Thank you very much for instructions.

 

Bests

Faeze