Extract ROI time courses

Submitted by lhenriques on

Hi,

Regarding the function 'Extract ROI time courses' and defining a random atlases as AAL, Craddock or Dosenbach, the output MATLAB file 'ROISignals' does not have the matching dimmensions according to the choosen atlas. For example: choosing the AAL atlas (116 ROIs), the dimmensions of ROISignals.mat file for one specific patient should be 80 x 116 double instead of 80 x 100 double as it results.

This does not occur with all the data, and sometimes the file's dimmensions fit the atlas' dimmensions but it seems very random when it fits and when it does not.

Do you know why this is happening ?

Thanks for your help.

Laeticia

Hi,

Thanks for your reply.

Basically what I do is the following steps:

(1) In DPARSF Basic Edition I only choose the option 'Extract ROI time course' and I define the ROI atlas as AAL atlas (for example)

(2) Then I choose the folder containing the already (pre) processed NIFTI file and I press RUN

(3) The resulting files are saved in the already existing 'Results' folder (created when pre processing is done) as the ROISignals file

(4) Opening this file in MATLAB the dimmensions are 80 x 100 double which is not compatible with the dimmensions of AAL atlas file.

These results also occur choosing other atlas as Craddock 200 ROI.

I hope I have been clear, but if you have some doubts please let me know.

Thanks for your help.

Laeticia

scorpio

Sat, 10/05/2019 - 05:18

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I have similar errors when i use y_ExtractROISignal.m for batch, the output is not signals, but a vertor of integers (which i think might be labels in the ROI atlas).

I think you may check whether there is only one subject in your data folder?

if so, when extracting signals, the code y_ExtractROISignal.m (line 154) that DPARSF uses might wrongly take the ROI atlas as Seed Series Definition, but not masks. 

so, you could try to have two or more subjects for extracting signals, to see if there are any other problems.

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