Wrong ROI definition when extracting CSF/WM signal etc

Submitted by aperry on Fri, 07/19/2013 - 11:17

Hello, I am receiving a bug when extracting the ROI signals (i.e white matter, CSF) for the nuisance covariates regression. The error appears after slice timing, realignment have been done. The error I received is below, I believe it is due to DPARSFA not being able to find the masks in the working directory. The error only appears with DPARSFA. My data was converted from DICOM --> NIFTI outside of DPARSF, then converted into spm format using freesurfers mri_convert to 208 indiviudal img files. The original raw data are as follows: Voxels: 128 x 128 x 29 Dimensions: 1.875 x 1.875 x 4.5mm.     ----------------------------------------------------------------------------------------------------------------------------                                                                                                      Generating voxel specific head motion for /home/alistair/Documents/dparsftest/RealignParameter/3994A/rp_aimg001.txt finished.
Generate voxel specific head motion: 3994A OK.
Extracting ROI signals...    
 Read 3D EPI functional images: "/home/alistair/Documents/dparsftest/FunImgAR/3994A"..........................................
Error using y_ExtractROISignal (line 188) Wrong ROI definition, please check: /home/alistair/Documents/dparsftest/Mask /3994A_BrainMask_05_91x109x91.nii
Error in DPARSFA_run>(parfor body) (line 1852)                 y_ExtractROISignal([AutoDataProcessParameter.DataProcessDir,filesep,FunSessionPrefixSet{iFunSession},AutoDataProcessParameter.StartingDirName,filesep,AutoDataProcessParameter.SubjectI                 Error in parallel_function (line 466)             F(base, limit); Error in DPARSFA_run (line 1753)         parfor i=1:AutoDataProcessParameter.SubjectNum Error in DPARSFA>pushbuttonRun_Callback (line 1579)     [Error]=DPARSFA_run(handles.Cfg); Error in gui_mainfcn (line 96)         feval(varargin{:}); Error in DPARSFA (line 33)     gui_mainfcn(gui_State, varargin{:});   Error while evaluating uicontrol Callback

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YAN Chao-Gan

Fri, 07/19/2013 - 15:34

I thinks it's the problem of your DPARSFA setting (i.e., missed "Segmentation/New Segmentation+DARTEL"). Please paste a snapshot here.

aperry

Sat, 07/20/2013 - 01:15

aperry

Sat, 07/20/2013 - 01:19

I do not wish to use T1 information. But, what are the benefits? 

I gather that T1 files are compulsory if it use to wish the preprocessing steps of DPARSFA. I have been able to do the pre-processing within the original DPARSF, and extract functional connectivity matrices via DPARSFA.

Alistair

YAN Chao-Gan

Wed, 07/24/2013 - 20:38

If you want to do it as basic edition (without T1 image), you need to do nuisance regression after spatial normalization (Course Part III).

Best,

Chao-Gan