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Amir, Looks like the functional and anatomical are not aligned. Make sure that the origin and rotation of the anatomical/template (if warping straight to epi template) and functional data are roughly the same. Alternatively, the subject shown may have been acquired incorrectly. Check the raw data before processing to make sure the whole brain is there. Best, Donald > On Jan 7, 2017, at 8:27 AM, Amir Dehsarvi <[log in to unmask]> wrote: > > Dear SPM experts, > > I am trying to analyse some data taken from PPMI. I have downloaded the rs-fMRI 4D nifti files and T1 MRI scans of the same subjects. I would like to do a DCM analysis on the data, however, unfortunately, I get errors half way through the preprocessing, when I try to extract the PCC, mPFC, LIPC, and RIPC time series. I had a look at the masks and they look totally different (and useless) from the masks that I had generated on previous datasets (see attached file). The data is basically downloaded in folders according to each subject and subfolders based on different sessions. Therefore, I had to do some folder organisation to adapt it to the normal SPM folder format according to the manual (I have put the T1 images in a folder called "anat" and the rs-fMRI images in a folder called "func")...On a different note, the TR and TE are 2400 and 25 based on the data collection protocol, but I changed them to 2.4 and .025, respectively. > > I was wondering whether anyone has used the PPMI data before (or any type of data of such raw basis), and if so, could you let me know how you did the organisation of the files in folders, preprocessing, and possibly the processing. Also, do you think I am doing something wrong in the analysis? > > Many thanks in advance, > I hope you are having a nice weekend, > Amir > > Amir Dehsarvi > PhD Student | Intelligent Systems Research Group | Department of Electronics | University of York > <Mask.png>