DPARSFA- Problem removing first time points and fieldmap correction

Submitted by MartheMie on Wed, 03/24/2021 - 15:16

Dear DPARSFA team,

first, I would like to thank you for your efforts with DPABI, I enjoy working with the toolbox. I hope I’m not sending questions that were already discussed and solved in the forum that I just hadn’t seen.

I encountered two problems for which I am kindly asking for advices.

  1. When I removed the first ten time points of the data the functional images look white pixelated, different from before remove. Before removing the time points the functional images looked as they used to look.
  2. When I did a fieldmap correction, I did it with the raw data (dicoms) and checked the boxes for doing it. After running the toolbox, I received the following error:

Error using DPARSFA_run (line 819)

Index exceeds the number of array elements (0).

 

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.

Maybe you might send me some hints what I could adapt to solve the problems.

 

Many thanks in advance.

Looking forward hearing from you.

 

Kind regards

Marthe

Forums:

YAN Chao-Gan

Fri, 03/26/2021 - 04:01

1. Is your data from Philips? I found sometimes there are problems for writing in int for Philips data. I will change this in the next release.

2. How did you organize your fieldmap data? Seems that's a data organization problem, you can use DPABI->Utilities->Check Data Organization.

MartheMie

Mon, 03/29/2021 - 13:22

Dear Prof. Chao-Gan,

I appreciate your reply and your help! Thank you for the helpful hints.

1) I am using data of a multicenter study including Philips (most), Siemens and GE scanner. The problem occured with Philips, some data measured with a Siemens but not GE. If I may ask you, if there is something I could to to solve the problem? Or is there an appropriate alternative?

2) I checked for the organization and as it seems this is the problem. If I may further ask: I have fieldmaps (T1 or T2 - I only used T1 and not T2) which are stored one dicom file. I tried the organization check with dicoms and niftis converted with dcm2niix (here the information that I have 1.imaginary 1.real 2.imaginary 2.real as niftis). However, I always get the error that something is wrong with my file organization. I also checked the explanation for organization that occurs when fieldmap correction is selected in DPARSFA but, I can't find a phase or magnitude image in my data. May I ask you for a hint what I can do best?

Thank you and grateful regards

Marthe

YAN Chao-Gan

Fri, 04/02/2021 - 01:49

1. You can download the developing version: https://github.com/Chaogan-Yan/DPABI

2. You have to convert the real and imaginary into phase and magnitude images. E.g., matlab command: abs() angle()

MartheMie

Fri, 04/09/2021 - 11:04

Dear Prof. Chao-Gan,

I could solve the problem! Thanks a lot for your reply and help.

Kind regards

Marthe

MartheMie

Mon, 05/03/2021 - 11:20

Dear Prof. Chao-Gan,

a further question came up and I kindly ask for another advice. Because I didn't find any information on it, I hope I haven't missed the answer to my question. As far as I know data can't be unwarped with DPARSFA, or is it possible? Otherwise, do I need to do the realignment and unwarping in SPM 12? What is your advice regarding the implementation of unwarping?

Many thanks in advance!

Kind regards,

Marthe

 

MartheMie

Thu, 05/06/2021 - 14:32

Dear Prof. Chao-Gan,

I'm sorry to bother you again but I faced a problem/ error while extracting the ROI signals using the ROI signal extractor (under utilities). I ran ReHo, fALFF and DC analyses in DPARSFA and now I would like to extract two ROIs. I also used the functional connectivity analyses and the extraction of ROI time courses in DPARSFA (for that I didn't have any problems with the ROI extraction).

When I'm using the ROI signal extractor  (utilities) I'm uploading e.g a nifti result map file of the DC analysis (DegreeCentrality_FunImgARCWFB) of a participant. And then I'm defining the ROIs (in my case the same nifti files I used for the extraction of ROI time courses before in DPARSFA), these are also nifti files including my two anatomical ROI regions that I extracted with marsbar from my used atlas. In the following I'm running the ROI extraction but then the following error occurs:

Error using y_ExtractROISignal (line 240)
Unrecognized function or variable 'MaskROILabel'.

Error in DPABI_ROISignalExtracter>ComputeButton_Callback (line 220)
parfor i=1:numel(ImgCells) %YAN Chao-Gan, 190105. Here don't need parfor. parfor i=1:numel(ImgCells)

MartheMie

Thu, 05/06/2021 - 14:34

Sorry it cut the rest of my text:

Error in gui_mainfcn (line 95)
        feval(varargin{:});
Error in DPABI_ROISignalExtracter (line 42)
    gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)DPABI_ROISignalExtracter('ComputeButton_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback.

As suggested in an answer to a question in the past in this forum, I used the break points in line 204 and the script ran until then but the variable MaskROILabel wasn't defined.

I am kindly asking for an advice, maybe you might send my a hint to solve my problem.

Thanks a lot in advance and wishing you a nice day.

Kind regards, Marthe

YAN Chao-Gan

Tue, 05/11/2021 - 04:24

From this message, seems you didn't define a correct ROI file correctly. Please check.

YAN Chao-Gan

Tue, 05/11/2021 - 04:23

You can use the FieldMap function in the latest DPARSFA.