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> Hi David, > > y_ExtractROISignal('./Filtered_4DVolume.nii', > {'/DPABI/Templates/AAL_61x73x61_YCG.nii'}, 'AALROITC', '', 1); > > Best, > > Chao-Gan > > > On Tue, Sep 2, 2014 at 2:34 PM, David Hofmann <[log in to unmask]> > wrote: > >> Hey Chao-Gan, >> >> this is exactly what I'm working on at the moment, e.g. extracting the >> ROI time courses from the AAL atlas supplied in the DPARSF templates >> folder. I tried to do this via GUI but had some problems. >> >> Do you mind giving an example of how to specify the function arguments in >> case of already "fully" pre-processed data and the AAL atlas file? That'll >> be helpful :) >> >> greetings >> >> David >> >> >> >> 2014-09-02 19:52 GMT+02:00 YAN Chao-Gan <[log in to unmask]>: >> >> Hi David, >>> >>> Alternatively, you can try >>> https://github.com/Chaogan-Yan/DPABI/blob/master/DPARSF_V3.0_140815/Subfunctions/y_ExtractROISignal.m >>> >>> >>> *% IsMultipleLabel - 1: There are multiple labels in the ROI mask file. >>> Will extract each of them. (e.g., for aal.nii, extract all the time series >>> for 116 regions)% 0 (default): All the non-zero values will be used to >>> define the only ROI* >>> >>> Best, >>> >>> Chao-Gan >>> >>> >>> >>> On Tue, Sep 2, 2014 at 1:48 PM, David Hofmann <[log in to unmask]> >>> wrote: >>> >>>> Hey Guillaume, >>>> >>>> does the spm_summarise function also work, when I have a nifti with >>>> multiple ROIs e.g. numbered 1-100 or is it necessary to run the function >>>> with seperate ROI nifti's? >>>> >>>> greetings >>>> >>>> David >>>> >>>> 2014-09-02 13:18 GMT+02:00 Guillaume Flandin <[log in to unmask]>: >>>> >>>> Dear Mahsa, >>>>> >>>>> if you want to mask your functional image with your ROI, you can indeed >>>>> use ImCalc as suggested by David (with expression i1.*i2) or >>>>> spm_mask.m. >>>>> >>>>> If you actually want to extract data from your functional image within >>>>> your ROI, you can use the spm_summarise function: >>>>> >> Y = spm_summarise('functional_image.nii','ROI.nii'); >>>>> >>>>> Best regards, >>>>> Guillaume. >>>>> >>>>> >>>>> On 31/08/14 12:32, Mahsa Alizade shalchy wrote: >>>>> > Dear all >>>>> > Hi >>>>> > Thank you so much for your time.I was able to create a mask of my >>>>> > desired ROIs(within MNI) using SPM(pickatlas).However,I could not >>>>> > extract the created ROI out of another image(i.e functional >>>>> > image)automatically and I have to multiply them using a matlab mfile >>>>> as >>>>> > following: >>>>> > Masked_image=ROI * image. >>>>> > How could I extract masked_image automatically? >>>>> > I searched through the older posts and came across"peak_extract_nii |